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Reverse Transformation and Martini v2.2P
- fabarca
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11 years 2 weeks ago #1541
by fabarca
Reverse Transformation and Martini v2.2P was created by fabarca
I'm trying to perform a reverse transformation of the last frame of my CG simulation (Protein+DPPC+PW+ION). But I got this error when I run g_fg2cg:
Name of CG water in topology should be W
Segmentation fault (core dumped)
Is g_fg2cg compatible with Martini v2.2P? If yes, How should I proceed to fix this problem?
Thanks
Name of CG water in topology should be W
Segmentation fault (core dumped)
Is g_fg2cg compatible with Martini v2.2P? If yes, How should I proceed to fix this problem?
Thanks
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- Clement
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11 years 2 weeks ago #1542
by Clement
Replied by Clement on topic Reverse Transformation and Martini v2.2P
1) Remove all (grep -v) the WP/WM particules from the .gro file you're using to reverse transform this system. Don't forget to change the total number of particules of your system (second line of the .gro file).
2) Call them W in your topology, as required by GROMACS.
2) Call them W in your topology, as required by GROMACS.
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- fabarca
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11 years 1 week ago #1551
by fabarca
Replied by fabarca on topic Reverse Transformation and Martini v2.2P
Thank you for your answer. I removed all lines with WP and WM from the .gro file. I also renamed PW to W in this file. I performed equivalent changes in the topology file cg.top and in martini_v2.2P.itp:
cg.top
#include "martini_v2.2P_fix.itp"
#include "Protein_A.itp"
#include "martini_v2.0_lipids.itp"
#include "martini_v2.0_ions.itp"
[ molecules ]
; name number
Protein_A 1
DPPC 256
W 5923
NA+ 95
CL- 96
martini_v2.2P.itp
;;;;;; POLARIZABLE WATER
[ moleculetype ]
; molname nrexcl
W 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 POL 1 W W 1 0
; 2 D 1 PW WP 1 0.46
; 3 D 1 PW WM 1 -0.46
But when I ran g_fg2cg, I got this error:
Program g_fg2cg, VERSION 3.3.1
Source code file: ../kernel/toputil.c, line: 61
Fatal error:
Atomtype 'LC3' not found!
So I tried to use the same forcefield that in the tutorial "top/ffDPPC.itp" instead of "ffG43a2m.itp" :
topol.top
#include "top/ffDPPC.itp"
#include "dppc.itp"
#include "fg_w.itp"
I also included two one-to-one mapping files, one for NA+ and one for Cl- (I tried to map solvatation waters but it didn't work).
With these changes I could run g_fg2cg and create a fg.gro file, however the message "Name of CG water in topology should be W" still appears. But now I have two new problems:
The first is that some amino acids are created several nm away from the protein, although this problem is fixed during SA protocol, the final FG structure doesn't resemble to the CG structures (in terms of the CA positions).
The second problem is that when I try to run g_fg2cg with another system that contains 4 protein instead of 1 (following these same steps), I got this error again, and the fg.gro file isn't created:
Name of CG water in topology should be W
Segmentation fault (core dumped)
I will be very grateful if you could help me.
cg.top
#include "martini_v2.2P_fix.itp"
#include "Protein_A.itp"
#include "martini_v2.0_lipids.itp"
#include "martini_v2.0_ions.itp"
[ molecules ]
; name number
Protein_A 1
DPPC 256
W 5923
NA+ 95
CL- 96
martini_v2.2P.itp
;;;;;; POLARIZABLE WATER
[ moleculetype ]
; molname nrexcl
W 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 POL 1 W W 1 0
; 2 D 1 PW WP 1 0.46
; 3 D 1 PW WM 1 -0.46
But when I ran g_fg2cg, I got this error:
Program g_fg2cg, VERSION 3.3.1
Source code file: ../kernel/toputil.c, line: 61
Fatal error:
Atomtype 'LC3' not found!
So I tried to use the same forcefield that in the tutorial "top/ffDPPC.itp" instead of "ffG43a2m.itp" :
topol.top
#include "top/ffDPPC.itp"
#include "dppc.itp"
#include "fg_w.itp"
I also included two one-to-one mapping files, one for NA+ and one for Cl- (I tried to map solvatation waters but it didn't work).
With these changes I could run g_fg2cg and create a fg.gro file, however the message "Name of CG water in topology should be W" still appears. But now I have two new problems:
The first is that some amino acids are created several nm away from the protein, although this problem is fixed during SA protocol, the final FG structure doesn't resemble to the CG structures (in terms of the CA positions).
The second problem is that when I try to run g_fg2cg with another system that contains 4 protein instead of 1 (following these same steps), I got this error again, and the fg.gro file isn't created:
Name of CG water in topology should be W
Segmentation fault (core dumped)
I will be very grateful if you could help me.
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- Clement
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11 years 1 week ago #1555
by Clement
Replied by Clement on topic Reverse Transformation and Martini v2.2P
Hi fabarca,
Sorry for the long absence. Busy busy.
I'm wondering what "the final FG structure doesn't resemble to the CG structures (in terms of the CA positions)" means. Can you quantify that? With a RMSD or so... The reverse-mapped structure won't be exactly the same as the CG conformation; the simulated annealing is moving everything around (should be in a reasonable extent though).
I can't really help with your second question about the segmentation fault problem... This error is sadly impossible to decrypt. You (and I) need more informations to get what's going wrong in there. If you did exactly the same steps (changing the name of water beads and such), should work the same. Check the files again, try to reproduce the error...
Sorry for the long absence. Busy busy.
I'm wondering what "the final FG structure doesn't resemble to the CG structures (in terms of the CA positions)" means. Can you quantify that? With a RMSD or so... The reverse-mapped structure won't be exactly the same as the CG conformation; the simulated annealing is moving everything around (should be in a reasonable extent though).
I can't really help with your second question about the segmentation fault problem... This error is sadly impossible to decrypt. You (and I) need more informations to get what's going wrong in there. If you did exactly the same steps (changing the name of water beads and such), should work the same. Check the files again, try to reproduce the error...
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