Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id
Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz < cos...@cim.sld.cu> wrote: > Hi all, > > I have a PDB file containing two proteins. One of the proteins has a long > stretch of missing residues. When I try to energy-minimize it, I get the > following: > > WARNING: Listed nonbonded interaction between particles 2897 and 2908 > at distance 3f which is larger than the table limit 3f nm. > > Now, it turns out that atoms 2897 and 2908 belong to the residues between > which the missing sequence lies. They are very far apart (because the > missing stretch is quite long), so I don't think there should be any > interaction between them. However, this WARNING seems to be saying that for > some reason, the topology generated included an interaction between them, > probably because it interpreted that since the two residues are consecutive > in the PDB file, they are bonded (which they aren't, because of the missing > residues). > > After trying some things, I realized that if I remove the option > "-chainsep id" from pdb2gmx when I generate the topology, I don't get this > warning. Instead, I get a bunch of topology files, each corresponding to a > fragment of each chain, instead of a topology per chain. This is very hard > to deal with, because, for example, if I want to make a position restrain > on the backbone of each chain, I have to keep track of each fragment > separately. > > Is there a way to fix the WARNING above without having to remove the > option "-chainsep id" from pdb2gmx? > > Thanks. Best, > cossio > --------------------------------------------------- > > [http://5.cim.co.cu/cim.gif] > -- > 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.