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using reverse transformation or backward tool
- jhosamelly
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9 years 10 months ago - 9 years 10 months ago #3802
by jhosamelly
using reverse transformation or backward tool was created by jhosamelly
I need to convert a Martini CG model to an All-Atom type model
this is the topology.
#include "martini_v2.1.itp"
#include "martini_v2.0_lipids.itp"
[ system ]
BILAYER SELF-ASSEMBLY
[ molecules ]
DSPC 32
DOPC 32
DPPC 32
DLPC 32
W 1500
i tried using the backward tool with this command
./initram.sh -f confout.gro -p aa.top -to gromos53a6 -keep
but there's an error
raise ValueError, "Unknown residue: %s\n"%resn
ValueError: Unknown residue: DSPC
...............
so I tried using reverse transformation but I can't seem to use the g_fg2cg command.
I'm using gromacs 4.6.5 ... :(
help please?
this is the topology.
#include "martini_v2.1.itp"
#include "martini_v2.0_lipids.itp"
[ system ]
BILAYER SELF-ASSEMBLY
[ molecules ]
DSPC 32
DOPC 32
DPPC 32
DLPC 32
W 1500
i tried using the backward tool with this command
./initram.sh -f confout.gro -p aa.top -to gromos53a6 -keep
but there's an error
raise ValueError, "Unknown residue: %s\n"%resn
ValueError: Unknown residue: DSPC
...............
so I tried using reverse transformation but I can't seem to use the g_fg2cg command.
I'm using gromacs 4.6.5 ... :(
help please?
Last edit: 9 years 10 months ago by jhosamelly.
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- Clement
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9 years 10 months ago #3803
by Clement
Replied by Clement on topic using reverse transformation or backward tool
This is the CG system topology. You need to provide the AA system topology (compound names might be slightly different, and the "#include"s at the beginning definitely different).
And g_fg2cg is only present in one tweaked version of GROMACS 3.3.3 available on this website...
And g_fg2cg is only present in one tweaked version of GROMACS 3.3.3 available on this website...
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- tsjerk
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9 years 10 months ago #3804
by tsjerk
Replied by tsjerk on topic using reverse transformation or backward tool
The mapping of DSPC is not yet available. It's not too hard to add it. You can contact me by mail if that doesn't work out for you.
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- jhosamelly
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9 years 10 months ago #3805
by jhosamelly
Replied by jhosamelly on topic using reverse transformation or backward tool
Thank you. I'll try reverse transformation again. Can I install it even though I have gromacs 4.6.5?? Thanks
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- jhosamelly
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9 years 10 months ago #3806
by jhosamelly
Replied by jhosamelly on topic using reverse transformation or backward tool
@tsjerk Thanks! How can I email you?
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- tsjerk
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9 years 10 months ago #3807
by tsjerk
Replied by tsjerk on topic using reverse transformation or backward tool
Yes, you can install multiple versions of Gromacs. Just make sure to set the correct installation directories.
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9 years 10 months ago #3808
by tsjerk
Replied by tsjerk on topic using reverse transformation or backward tool
You can drop a line to tsjerkw at gmail.
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- khuongtg
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8 years 10 months ago #4568
by khuongtg
Replied by khuongtg on topic using reverse transformation or backward tool
Hi tsjerk,
I also get the similar error "Unknow residue: PPCS". Can you help me with the mapping of PPCS?
I also get the similar error "Unknow residue: PPCS". Can you help me with the mapping of PPCS?
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- mferraro
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8 years 3 months ago #5339
by mferraro
Replied by mferraro on topic using reverse transformation or backward tool
Hello Tsjerk, I'm interested in mapping DSPC to an atomistic description too. I was wondering if mapping parameters for this lipid are still unavailable.
I've already searched for them without any luck.
Thanks in advance for you precious collaboration.
M.
I've already searched for them without any luck.
Thanks in advance for you precious collaboration.
M.
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