Mark, Thanks Mark! Indeed it was the problem. I forgot to update residuetypes.dat.
Regards, Simon 2017-05-12 15:46 GMT+08:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > Those define your residue, but do not classify it, so pdb2gmx doesn't know > that protein-specific termini are appropriate. > > From the link I provided: "Add your residue to residuetypes.dat with the > appropriate specification (Protein, DNA, Ion, etc)." > > Mark > > On Fri, May 12, 2017 at 9:39 AM Simon Kit Sang Chu <simoncks1...@gmail.com > > > wrote: > > > Dear Mark, > > > > Thanks for your prompt reply. I have already updated my .rtp and .hdb for > > my new residue. Would you mind to suggest which file I am missing? > > > > I am happy to provide relevant parts of .rtp and .hdb if necessary. > > > > Regards, > > Simon > > > > 2017-05-12 15:31 GMT+08:00 Mark Abraham <mark.j.abra...@gmail.com>: > > > > > Hi, > > > > > > I suspect you need to add your residue to the class of Protein > residues, > > > per > > > http://www.gromacs.org/Documentation/How-tos/Adding_ > > > a_Residue_to_a_Force_Field > > > > > > Mark > > > > > > On Fri, May 12, 2017 at 9:05 AM Simon Kit Sang Chu < > > simoncks1...@gmail.com > > > > > > > wrote: > > > > > > > Hi everyone, > > > > > > > > I am using a new forcefield which does not give proper neutral > capping, > > > but > > > > requires me to create a custom made residue for that purpose. > > > Specifically, > > > > I want a NH2 cap instead of NH+. > > > > > > > > I rename VAL1 into VAT1, update .hdb & .rtp. However, when I pdb2gmx > > -ter > > > > to create a topology file (none cap for N-terminal, COO- cap for > > > > C-terminal), the error warns missing hydrogen atom in GLY2. If I > chose > > > NH+ > > > > cap and COO- cap, the N+ occurs in GLY2 instead of VAT1. I believe > the > > > > capping option does not recognize the new residue VAT from the > > beginning. > > > > > > > > Is there any file the capping code depends on, to add my new residue > > VAT? > > > > > > > > Regards, > > > > Simon > > > > -- > > > > 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. > > > > > -- > > 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. > -- 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.