Force field in gromacs reads only standard amino acids/DNA/RNA residue. In your pdb file residue name XXX is not defined in gromos ff. If your system is other than protein then use ATB to generate topolgy.
<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Fri, Nov 3, 2017 at 2:19 PM, Adriano Santana Sanchez < adriano.santanasanc...@kaust.edu.sa> wrote: > Dear all, > > I am a beginner with gromacs and I have already done some online > tutorials. > I am now trying to create from a PDB coordinate file (a CTAB molecule) the > corresponding .GRO and .TOP files to run MD simulations. > > gmx pdb2gmx -f ctab.pdb -o ctab_processed.gro -water spce > > then choose FF gromos96 53a6 but get error message: > > Residue 'XXX' not found in topology database > > I am sure this FF has been used for this molecule before and I cannot > > find this CTAB on the residue database. What can I do? > > Thanks, > Adriano > > -- > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -- > 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.