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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