Reverse CG with Amber

xavier
Offline
Admin

13 years 2 months ago #495 by xavier

Replied by xavier on topic Reverse CG with Amber

is wrote:
andrzej wrote: There still must be something wrong in your topology. You can debug it by parts, so first check if g_cg2fg works only for the pep_A, then for pep_A + pep_B , at the end add water. When the mappings are correctly set and there is no ions, everything should run smoothly.

In the fg_w.itp four atomistic water molecules are bundled into one artificial water "cluster" which corresponds to one CG water. Thus the number of water molecules in topology notation is the same.

I included only Protein_A in both top files and gro file, and I get segmentation fault:
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
NOTE:
System has non-zero total charge: -9.000003e+00

# BONDS: 5200
# ANGLES: 9417
# PDIHS: 1013
# RBDIHS: 10681
# LJ14: 13541
calling cpp...
processing topology...
Generated 4 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for Protein_A 1
NOTE:
System has non-zero total charge: -9.000000e+00

Number of fg atoms 5151
Number of cg atoms 711
Reading frames from gro file 'Giving Russians Opium May Alter Current Situation', 711 atoms.
Reading frame 0 time 0.000 1296061305
Name of CG water in topology should be W
Segmentation fault

Those are my top files:
fg:

; Include forcefield parameters
#include "ffamber03.itp"

; Include chain topologies
#include "prot_A.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound #mols
Protein_A 1

and cg:

; Include forcefield parameters
#include "martini_v2.1.itp"
#include "prot_cg.itp"

[ system ]
; name
Protein

[ molecules ]
; name number
Protein_A 1

So they, as well as cg .gro file, look fine. What can be wrong?

I guess your CG trajectory should only contain the protein_A right!

is

Please Log in or Create an account to join the conversation.

is
Topic Author
Offline
Senior Boarder

13 years 2 months ago #496 by is

Replied by is on topic Reverse CG with Amber

xavier wrote:
is wrote:
andrzej wrote: There still must be something wrong in your topology. You can debug it by parts, so first check if g_cg2fg works only for the pep_A, then for pep_A + pep_B , at the end add water. When the mappings are correctly set and there is no ions, everything should run smoothly.

In the fg_w.itp four atomistic water molecules are bundled into one artificial water "cluster" which corresponds to one CG water. Thus the number of water molecules in topology notation is the same.

I included only Protein_A in both top files and gro file, and I get segmentation fault:
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
NOTE:
System has non-zero total charge: -9.000003e+00

# BONDS: 5200
# ANGLES: 9417
# PDIHS: 1013
# RBDIHS: 10681
# LJ14: 13541
calling cpp...
processing topology...
Generated 4 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours for Protein_A 1
NOTE:
System has non-zero total charge: -9.000000e+00

Number of fg atoms 5151
Number of cg atoms 711
Reading frames from gro file 'Giving Russians Opium May Alter Current Situation', 711 atoms.
Reading frame 0 time 0.000 1296061305
Name of CG water in topology should be W
Segmentation fault

Those are my top files:
fg:

; Include forcefield parameters
#include "ffamber03.itp"

; Include chain topologies
#include "prot_A.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound #mols
Protein_A 1

and cg:

; Include forcefield parameters
#include "martini_v2.1.itp"
#include "prot_cg.itp"

[ system ]
; name
Protein

[ molecules ]
; name number
Protein_A 1

So they, as well as cg .gro file, look fine. What can be wrong?
I guess your CG trajectory should only contain the protein_A right!
is

Yes, but at this stage I do not include trajectory file. I have still problem with reversing cg to fg.

Please Log in or Create an account to join the conversation.

xavier
Offline
Admin

13 years 2 months ago #497 by xavier

Replied by xavier on topic Reverse CG with Amber

is wrote: Yes, but at this stage I do not include trajectory file. I have still problem with reversing cg to fg.

Ok, but then your gro file should contain only the protein_A!
If not you have a problem in your topology ... no doubt about it!

Please Log in or Create an account to join the conversation.

is
Topic Author
Offline
Senior Boarder

13 years 2 months ago #498 by is

Replied by is on topic Reverse CG with Amber

xavier wrote:
is wrote: Yes, but at this stage I do not include trajectory file. I have still problem with reversing cg to fg.

Ok, but then your gro file should contain only the protein_A!
If not you have a problem in your topology ... no doubt about it!

It contains only Protain_A, as I wrote before.
Any other suggestions?

Please Log in or Create an account to join the conversation.

xavier
Offline
Admin

13 years 2 months ago #499 by xavier

Replied by xavier on topic Reverse CG with Amber

is wrote:
xavier wrote:
is wrote: Yes, but at this stage I do not include trajectory file. I have still problem with reversing cg to fg.

Ok, but then your gro file should contain only the protein_A!
If not you have a problem in your topology ... no doubt about it!

It contains only Protain_A, as I wrote before.
Any other suggestions?

Number of atoms in cg.gro correct?

I actually have no clue what is going wrong! Could be a lot of things.
Try to start again from scratch ... you may have introduced some silly thing at some point ...

Please Log in or Create an account to join the conversation.

is
Topic Author
Offline
Senior Boarder

13 years 2 months ago #500 by is

Replied by is on topic Reverse CG with Amber

xavier wrote:
is wrote:
xavier wrote:
is wrote: Yes, but at this stage I do not include trajectory file. I have still problem with reversing cg to fg.

Ok, but then your gro file should contain only the protein_A!
If not you have a problem in your topology ... no doubt about it!

It contains only Protain_A, as I wrote before.
Any other suggestions?

Number of atoms in cg.gro correct?

I actually have no clue what is going wrong! Could be a lot of things.
Try to start again from scratch ... you may have introduced some silly thing at some point ...

Yes, number is correct.

Please Log in or Create an account to join the conversation.

is
Topic Author
Offline
Senior Boarder

13 years 2 months ago #501 by is

Replied by is on topic Reverse CG with Amber

Can Gromacs version cause those problems, as reverse transformation is done using v. 3.3.1, while simulation was performed using v. 4.0.7.?

Please Log in or Create an account to join the conversation.

xavier
Offline
Admin

13 years 2 months ago #502 by xavier

Replied by xavier on topic Reverse CG with Amber

is wrote: Can Gromacs version cause those problems, as reverse transformation is done using v. 3.3.1, while simulation was performed using v. 4.0.7.?

I am not sure how this could be the case. The only thing you are using from a 4.0.7 version is a gro file!

You might want to check your mapping and your protein topologies.

May be Andrzej hasa better idea!

Please Log in or Create an account to join the conversation.

is
Topic Author
Offline
Senior Boarder

13 years 2 months ago #503 by is

Replied by is on topic Reverse CG with Amber

Yes, but also all atom .itp files for Protein_A and Protein_B.

Please Log in or Create an account to join the conversation.

xavier
Offline
Admin

13 years 2 months ago #504 by xavier

Replied by xavier on topic Reverse CG with Amber

is wrote: Yes, but also all atom .itp files for Protein_A and Protein_B.

The topology itself should not be a problem but the way the topol.top file is made is different. Try to grompp you protein topology!

Please Log in or Create an account to join the conversation.

andrzej
Visitor

13 years 2 months ago #505 by andrzej

Replied by andrzej on topic Reverse CG with Amber

This segmentation fault can only be caused by ill defined mapping. Please check the mapping section in the atomistic protein_A (and protein_B) itp file. All atoms present in the system (so in the gro file) should be assigned to one of the cg beads. The mapping is automatically created by the modified pdb2gmx ( as explained in the paper) and information about mapping is taken from rtp file of the forcefield. Did You include mapping to the rtp of amber forcefiled ? Its not difficult, when you need more help please write

Andrzej

Please Log in or Create an account to join the conversation.

is
Topic Author
Offline
Senior Boarder

13 years 2 months ago #506 by is

Replied by is on topic Reverse CG with Amber

andrzej wrote: This segmentation fault can only be caused by ill defined mapping. Please check the mapping section in the atomistic protein_A (and protein_B) itp file. All atoms present in the system (so in the gro file) should be assigned to one of the cg beads. The mapping is automatically created by the modified pdb2gmx ( as explained in the paper) and information about mapping is taken from rtp file of the forcefield. Did You include mapping to the rtp of amber forcefiled ? Its not difficult, when you need more help please write

Andrzej

So, this might be an issue.
To generate CG structure and all top and itp files I used MARTINI scripts proposed in "Protein in water" tutorial. After performing simulation, I decided I would like to do RV-CG. That's why I didn't use pdb2gmx tool (Gromacs 3.x.x. v.).
So, it means that I'm missing mapping section that can only be generated by this pdb2gmx tool? Can I generate this section, by pdb2gmx tool and simply put it into my already existing topology file? I would expect that only difference between this two top files (generated by pdb2gmx and MARTINI script) would be a mapping section?

Please Log in or Create an account to join the conversation.

xavier
Offline
Admin

13 years 2 months ago #507 by xavier

Replied by xavier on topic Reverse CG with Amber

is wrote:
andrzej wrote: This segmentation fault can only be caused by ill defined mapping. Please check the mapping section in the atomistic protein_A (and protein_B) itp file. All atoms present in the system (so in the gro file) should be assigned to one of the cg beads. The mapping is automatically created by the modified pdb2gmx ( as explained in the paper) and information about mapping is taken from rtp file of the forcefield. Did You include mapping to the rtp of amber forcefiled ? Its not difficult, when you need more help please write

Andrzej

So, this might be an issue.
To generate CG structure and all top and itp files I used MARTINI scripts proposed in "Protein in water" tutorial. After performing simulation, I decided I would like to do RV-CG. That's why I didn't use pdb2gmx tool (Gromacs 3.x.x. v.).
So, it means that I'm missing mapping section that can only be generated by this pdb2gmx tool? Can I generate this section, by pdb2gmx tool and simply put it into my already existing topology file? I would expect that only difference between this two top files (generated by pdb2gmx and MARTINI script) would be a mapping section?

in my first answer to you I asked you this:
"Did you manage to implement the mapping for the Amber force field?"

The definition of the mapping between the two force fields (cg/Atomistic) is of course of primary importance and the basis of the all process.

Going through the tutorial would be a excellent start :))

Andrzej has implemented the mapping between Martini and a gromos FF (only one version if I am correct). You could get inspired from that and get the Amber FF done. That would be useful!

Please Log in or Create an account to join the conversation.

is
Topic Author
Offline
Senior Boarder

13 years 2 months ago #508 by is

Replied by is on topic Reverse CG with Amber

xavier wrote:
is wrote:
andrzej wrote: This segmentation fault can only be caused by ill defined mapping. Please check the mapping section in the atomistic protein_A (and protein_B) itp file. All atoms present in the system (so in the gro file) should be assigned to one of the cg beads. The mapping is automatically created by the modified pdb2gmx ( as explained in the paper) and information about mapping is taken from rtp file of the forcefield. Did You include mapping to the rtp of amber forcefiled ? Its not difficult, when you need more help please write

Andrzej

So, this might be an issue.
To generate CG structure and all top and itp files I used MARTINI scripts proposed in "Protein in water" tutorial. After performing simulation, I decided I would like to do RV-CG. That's why I didn't use pdb2gmx tool (Gromacs 3.x.x. v.).
So, it means that I'm missing mapping section that can only be generated by this pdb2gmx tool? Can I generate this section, by pdb2gmx tool and simply put it into my already existing topology file? I would expect that only difference between this two top files (generated by pdb2gmx and MARTINI script) would be a mapping section?

in my first answer to you I asked you this:
"Did you manage to implement the mapping for the Amber force field?"

The definition of the mapping between the two force fields (cg/Atomistic) is of course of primary importance and the basis of the all process.

Going through the tutorial would be a excellent start :))

Andrzej has implemented the mapping between Martini and a gromos FF (only one version if I am correct). You could get inspired from that and get the Amber FF done. That would be useful!

Yes, you are right.
I misunderstood the question about Amber mapping.
I would like to kindly ask for this mapping between Martini and Gromos ff. However, I don't know if I can do it, but I would at least like to try.

Please Log in or Create an account to join the conversation.

xavier
Offline
Admin

13 years 2 months ago #509 by xavier

Replied by xavier on topic Reverse CG with Amber

is wrote: Yes, you are right.
I misunderstood the question about Amber mapping.
I would like to kindly ask for this mapping between Martini and Gromos ff. However, I don't know if I can do it, but I would at least like to try.

No problem ... no we know what was wrong :))

The mapping between Martini and Gromos 43a2 and 53a6 can be found in the share/top directory of the modified version of gromacs-3.3.1. You have to open the rtp file and
look for the [ mapping ] section. The files corresponding to the "reverse transformation" have an extra "m"; eg: ffG43a2.rtp becomes ffG43a2m.rpt. There is supposed to be a mapping for each relevant molecule: amino acids, lipids, water ...

Note that you may be facing a problem that is the Amber FF uses potential forms that may not be implemented in gmx-3.3.1. They are is older versions of gmx, 407 for example. Just make sure the Amber FF is fine in gmx331.

Let us know how it goes and if we can be of any help ... this might be of interest for more people in the future.

XAvier.

Please Log in or Create an account to join the conversation.

is
Topic Author
Offline
Senior Boarder

13 years 2 months ago #510 by is

Replied by is on topic Reverse CG with Amber

Thank you, I will try to do it, and I will let you know how it goes.

Please Log in or Create an account to join the conversation.

is
Topic Author
Offline
Senior Boarder

13 years 2 months ago #525 by is

Replied by is on topic Reverse CG with Amber

xavier wrote:
is wrote: Yes, you are right.
I misunderstood the question about Amber mapping.
I would like to kindly ask for this mapping between Martini and Gromos ff. However, I don't know if I can do it, but I would at least like to try.

No problem ... no we know what was wrong :))

The mapping between Martini and Gromos 43a2 and 53a6 can be found in the share/top directory of the modified version of gromacs-3.3.1. You have to open the rtp file and
look for the [ mapping ] section. The files corresponding to the "reverse transformation" have an extra "m"; eg: ffG43a2.rtp becomes ffG43a2m.rpt. There is supposed to be a mapping for each relevant molecule: amino acids, lipids, water ...

Note that you may be facing a problem that is the Amber FF uses potential forms that may not be implemented in gmx-3.3.1. They are is older versions of gmx, 407 for example. Just make sure the Amber FF is fine in gmx331.

Let us know how it goes and if we can be of any help ... this might be of interest for more people in the future.

XAvier.

Hi XAvier,

So did as you suggested, I added mapping section for Amber in ffamber03m.rtp file for standard amino acids, I renamed files and linked them if necessary. However, I still get exactly the same error as before. How to check if gmx has potential forms for Amber ff?

is

Please Log in or Create an account to join the conversation.

xavier
Offline
Admin

13 years 2 months ago #526 by xavier

Replied by xavier on topic Reverse CG with Amber

is wrote: Hi XAvier,

So did as you suggested, I added mapping section for Amber in ffamber03m.rtp file for standard amino acids, I renamed files and linked them if necessary. However, I still get exactly the same error as before. How to check if gmx has potential forms for Amber ff?

is

Run an atomic simulation of your system. No need to rerun with gmx3.3.1, but a short run to check whether the amber force field is defined or not!

You may also want to go on the gromacs web site whether gmx3.3.1 has the amber force field you use implemented.

XAvier.

Please Log in or Create an account to join the conversation.

is
Topic Author
Offline
Senior Boarder

13 years 2 months ago #530 by is

Replied by is on topic Reverse CG with Amber

xavier wrote:
is wrote: Hi XAvier,

So did as you suggested, I added mapping section for Amber in ffamber03m.rtp file for standard amino acids, I renamed files and linked them if necessary. However, I still get exactly the same error as before. How to check if gmx has potential forms for Amber ff?

is
Run an atomic simulation of your system. No need to rerun with gmx3.3.1, but a short run to check whether the amber force field is defined or not!

You may also want to go on the gromacs web site whether gmx3.3.1 has the amber force field you use implemented.

XAvier.

So, there is no problem with atomistic simulation. Gromacs doesn't complain, and I can generate needed files.

Please Log in or Create an account to join the conversation.

xavier
Offline
Admin

13 years 2 months ago #531 by xavier

Replied by xavier on topic Reverse CG with Amber

is wrote:
xavier wrote:
is wrote: Hi XAvier,

So did as you suggested, I added mapping section for Amber in ffamber03m.rtp file for standard amino acids, I renamed files and linked them if necessary. However, I still get exactly the same error as before. How to check if gmx has potential forms for Amber ff?

is
Run an atomic simulation of your system. No need to rerun with gmx3.3.1, but a short run to check whether the amber force field is defined or not!

You may also want to go on the gromacs web site whether gmx3.3.1 has the amber force field you use implemented.

XAvier.

So, there is no problem with atomistic simulation. Gromacs doesn't complain, and I can generate needed files.

Ok so you should check your mapping.

As Andrzej said earlier every atom should be assigned to a CG bead. It is not fundamental when going from atomistic to CG but from CG to atomist it is.

Check and check again ... must be something funky somewhere :))

Please Log in or Create an account to join the conversation.

Time to create page: 0.136 seconds

General Purpose Coarse-Grained Force Field

Nav view search

Navigation

Reverse CG with Amber