On Tue, Apr 14, 2015 at 11:12 AM, Ming Tang <m21.t...@qut.edu.au> wrote:
> Hi Mark, > > Thanks for your reply. I am sure as I changed the files in the charmm27.ff > installed in my unbuntu system. Is there any other things I need to > consider? > pdb2gmx lists the full path to the folder in which it finds the files it is actually using. The most likely problem is that it's not finding what you think it is, and there are many and frequent ways that could happen. Please check that. Mark > Thanks, > Ming > > > -----Original Message----- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: Tuesday, 14 April 2015 6:53 PM > To: Discussion list for GROMACS users > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] adding SR2++ to charm27 force field > > Hi, > > Inspect the whole output. Is pdb2gmx picking up the version of charmm27 > you think it is? > > Mark > > On Tue, Apr 14, 2015 at 8:40 AM, Ming Tang <m21.t...@qut.edu.au> wrote: > > > Dear all, > > > > I am trying to add SR 2++ in charm27 force field. I modified the > > ffnonbonded.itp, ffnanonbonded.itp, ions.itp, aminoacids,rtp, > > atomtypes.atp according to the parameters of SR in oplsaa.ff. > > However, when using pdb2gmx, I came across the following fatal error: > > Atomtype SR not found. > > Could anybody give me some advice? > > > > Thanks in advance, > > Ming > > -- > > 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.
