Dear Gromacs Users, Justin, I took your advice and using 4.5.1.
I have attached the PDB file for your consideration. http://www.4shared.com/file/RwF_wuja/chainABCRST.html Command : newpdb2gmx -f chainABCRST.pdb -p dimertop.top -o dimerpdb.pdb -chainsep interactive -ignh 8: CHARMM27 all-atom force field (with CMAP) - version 2.0beta (forcefield selected) 6: None (water model) Reading chainABCRST.pdb... Read 6636 atoms Analyzing pdb file Splitting PDB chains based on TER records or changing chain id. Merge chain ending with residue LEU144 (chain id 'A', atom 1444 OXT) with chain starting with residue LYS284 (chain id 'B', atom 1445 N)? [n/y] y Merge chain ending with residue LEU427 (chain id 'B', atom 2888 OXT) with chain starting with residue LYS567 (chain id 'C', atom 2889 N)? [n/y] y Merge chain ending with residue LEU710 (chain id 'C', atom 4332 OXT) with chain starting with residue CYS145 (chain id 'R', atom 1 N)? [n/y] n Merge chain ending with residue CYS283 (chain id 'R', atom 1400 OXT) with chain starting with residue CYS428 (chain id 'S', atom 1401 N)? [n/y] y Merge chain ending with residue CYS566 (chain id 'S', atom 2800 OXT) with chain starting with residue CYS711 (chain id 'T', atom 2801 N)? [n/y] y Program newpdb2gmx, VERSION 4.5.1 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue LEU 427 was not found in rtp entry LEU with 19 atoms while sorting atoms. ********* But this selection works (for the same above command, 1 ) Merge chain ending with residue LEU144 (chain id 'A', atom 1444 OXT) with chain starting with residue LYS284 (chain id 'B', atom 1445 N)? [n/y] y Merge chain ending with residue LEU427 (chain id 'B', atom 2888 OXT) with chain starting with residue LYS567 (chain id 'C', atom 2889 N)? [n/y] n Merge chain ending with residue LEU710 (chain id 'C', atom 4332 OXT) with chain starting with residue CYS145 (chain id 'R', atom 1 N)? [n/y] y Merge chain ending with residue CYS283 (chain id 'R', atom 1400 OXT) with chain starting with residue CYS428 (chain id 'S', atom 1401 N)? [n/y] n Merge chain ending with residue CYS566 (chain id 'S', atom 2800 OXT) with chain starting with residue CYS711 (chain id 'T', atom 2801 N)? [n/y] y ************************* After ABC , I include a 'TER', then start chain RST, and make 'chainsep ter' 2. newpdb2gmx -f chainABCRSTter.pdb -p dimertop.top -o dimerpdb.pdb -chainsep ter -ignh Program newpdb2gmx, VERSION 4.5.1 Source code file: pdb2gmx.c, line: 655 Fatal error: Atom OXT in residue LEU 427 was not found in rtp entry LEU with 19 atoms while sorting atoms. The residue are not in sequential Order , but i dont think that is the problem here. Thank you. Best, nahren --- On Fri, 9/3/10, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] intermolecular distance restrains To: "Gromacs Users' List" <gmx-users@gromacs.org> Date: Friday, September 3, 2010, 3:18 AM nahren manuel wrote: > > Dear Gromacs Users, > > The problem actually is mine is a hexamer, ARBSCT (chains). I want RST to be > merged into a single molecular topology. I am either able to merge RS or ST > or RT but not the trimer as such. > How is the .pdb set up? Does it have both chain ID's and TER delimiters? What was your pdb2gmx command line? -Justin > I am able to do with -merge in the previous (ver 4.0.7 of ) pdb2gmx. > > Best, > nahren > > --- On *Thu, 9/2/10, Justin A. Lemkul /<jalem...@vt.edu>/* wrote: > > > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] intermolecular distance restrains > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Thursday, September 2, 2010, 8:09 PM > > > > nahren manuel wrote: > > Dear Gromacs Users, > > > > I am presently using gromacs4.5 beta(since I want implicit > solvent). I > > No need to use a beta version, the official 4.5 has been released. > > > wish to apply intermolecular distance restraints. > > To my surprise there is no merge option in pdb2gmx (although > pdb2gnx -h, says it has). So is there a new alternative to create > intermolecular distance restrains. > > > > Use pdb2gmx -chainsep. > > -Justin > > > Best, > > nahren > > > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org > </mc/compose?to=gmx-us...@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org > </mc/compose?to=gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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