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 > <suchitasakor...@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. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
