Peter, it should be in aminoacids, just a legacy file naming. Alex
On Mon, Jun 22, 2015 at 12:46 PM, Peter Stern <peter.st...@weizmann.ac.il> wrote: > Even though it's called aminoacids.n.tdb? Or a different name, e.g. > nucleicacids.n.tdb? > One problem is that I eventually have to deal with tens, maybe hundreds of > complexes. > Some, of course, will have the normal 5' nucleotide. Will I be able to > choose the appropriate n.tdb file for each case > or will I have to copy the appropriate one to my run directory each time? > I guess the latter. > > Thanks, > Peter > > -----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 Justin > Lemkul > Sent: Monday, June 22, 2015 9:39 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Get pdb2gmx not to treat the first nucleotide in > a chain as 5' > > > > On 6/22/15 2:36 PM, Peter Stern wrote: > > I have a chain of RNA in complex with a protein. > > The pdb file is missing the first two nucleotides and starts with the > third including the PO2 group. > > pdb2gmx identifies this as the 5' terminal nucleotide and tries to > create the topology from rna.rtp using RA5 as the "residue" type. > > Thus it doesn't like the fact that the coordinates contain a P atom and > fails. I would like to avoid removing the coordinates for PO2. > > How can I get pdb2gmx to treat the first (and last in other cases) > nucleotide as a "normal" residue? > > Simply changing the name of the residue from A to RA does not work. > > > > You'll need to create an entry in the .n.tdb file that specifies a > 5'-phosphate cap. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.
