[gmx-users] amb2gmx for big systems

[Rebeca García Fandiño]

Hello,
I am trying to convert a membrane-protein system from amber to gromacs using the script amb2gmx.pl (http://chemistry.csulb.edu/ffamber/tools.html).
It is the dry system, only the protein and a membrane composed by DOPC, whose parameters I have got from Gaff.
 
When I try:
 
./amb2gmx.pl --prmtop dry_system.top --crd dry_system.crd --outname dry_system_gmx
 
I get an error related to the “*” symbols in the pdb (I have 253.000 atoms):
(…)
Argument " NATOM or " isn't numeric in multiplication (*) at ./amb2gmx.pl line 200, <PDB> line 1.
Argument "NRES is to" isn't numeric in multiplication (*) at ./amb2gmx.pl line 201, <PDB> line 1.
Argument "o big:" isn't numeric in multiplication (*) at ./amb2gmx.pl line 202, <PDB> line 1.
substr outside of string at ./amb2gmx.pl line 205, <PDB> line 1.
Use of uninitialized value in addition (+) at ./amb2gmx.pl line 205, <PDB> line 1.
substr outside of string at ./amb2gmx.pl line 208, <PDB> line 1.
Use of uninitialized value in addition (+) at ./amb2gmx.pl line 208, <PDB> line 1.
substr outside of string at ./amb2gmx.pl line 209, <PDB> line 1.
Use of uninitialized value in addition (+) at ./amb2gmx.pl line 209, <PDB> line 1.
substr outside of string at ./amb2gmx.pl line 212, <PDB> line 1.
 
 
Is there a way to transform amber systems to gromacs in spite of the “*” symbols? Has anyone transformed this type of systems? How could I save the problem?
 
Thank you very much for your help in advance,
 
Rebeca García Fandiño
Parc Cientific de Barcelona
 
 
 
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