[gmx-users] issue regarding gromacs software

Valerio valerio.ferrario at gmail.com
Fri Feb 15 18:34:39 CET 2019

I do not see the attachment... Which forcefield are planning to use? In any case you should check the input pdb you are using: are the amino acid residues named in the proper way? It is a standard pdb? Do you have some non-natural amino acid or modified residue in your peptide? Moreover you should try to ignore hydrogens (-ignh) and to manually define the protonation state (-inter).

> Il giorno 15 feb 2019, alle ore 18:17, suchita sakore <suchitasakore00 at gmail.com> ha scritto:
> Respected sir/madam,
> I am doing a project under my post graduation.  I am doing a simulation of
> a lipid ion channel by using gromacs software. I am facing problem while
> generating the gro file. I have built peptide by using discovery studio
> software.
> while running the following command :
> gmx_mpi pdb2gmx -f pep.pdb -o pep.gro
> The error seen is that the molecule is undefined in the PDB format. The
> gromacs software is  not able to recognize the molecule. I am attaching
> here the file on which I am working right now. Kindly resolve my problem as
> soon as possible. I am waiting for your answer.
> Thanking you in anticipation.
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