AMBER Archive (2008)

Subject: AMBER: amb2gmx for big systems

From: rebeca_at_mmb.pcb.ub.es
Date: Thu Jul 31 2008 - 05:40:39 CDT

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).

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
rebeca_at_mmb.pcb.ub.es

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