<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Gromacs Users,<br><br>Justin, I took your advice and using 4.5.1. <br><br>I have attached the PDB file for your consideration.<br>http://www.4shared.com/file/RwF_wuja/chainABCRST.html<br><br>Command : newpdb2gmx -f chainABCRST.pdb -p dimertop.top -o dimerpdb.pdb -chainsep interactive -ignh<br><br>8: CHARMM27 all-atom force field (with CMAP) - version 2.0beta (forcefield selected)<br><br>6: None (water model)<br><br>Reading chainABCRST.pdb...<br>Read 6636 atoms<br>Analyzing pdb file<br>Splitting PDB chains based on TER records or changing chain id.<br>Merge chain ending with residue LEU144 (chain id 'A', atom 1444 OXT) with<br>chain starting with residue LYS284 (chain id 'B', atom 1445 N)? [n/y]<br>y<br>Merge chain ending with residue LEU427 (chain id 'B', atom 2888 OXT) with<br>chain starting with residue LYS567 (chain id 'C', atom 2889
N)? [n/y]<br>y<br>Merge chain ending with residue LEU710
(chain id 'C', atom 4332 OXT) with<br>chain starting with residue CYS145 (chain id 'R', atom 1 N)? [n/y]<br>n<br>Merge chain ending with residue CYS283 (chain id 'R', atom 1400 OXT) with<br>chain starting with residue CYS428 (chain id 'S', atom 1401 N)? [n/y]<br>y<br>Merge chain ending with residue CYS566 (chain id 'S', atom 2800 OXT) with<br>chain starting with residue CYS711 (chain id 'T', atom 2801 N)? [n/y]<br>y<br><br>Program newpdb2gmx, VERSION 4.5.1<br>Source code file: pdb2gmx.c, line: 655<br><br><span style="border-bottom: 2px dotted rgb(54, 99, 136); cursor: pointer;" class="yshortcuts" id="lw_1283506479_0">Fatal error</span>:<br>Atom OXT in residue LEU 427 was not found in rtp entry LEU with 19 atoms<br>while sorting atoms.<br><br>*********<br>But this selection works (for the same above command, 1 )<br><br>Merge chain ending with residue LEU144 (chain id 'A', atom 1444 OXT) with<br>chain starting with residue LYS284 (chain id 'B', atom 1445
N)? [n/y]<br>y<br>Merge chain ending with residue LEU427 (chain id 'B', atom 2888 OXT) with<br>chain starting with residue
LYS567 (chain id 'C', atom 2889 N)? [n/y]<br>n<br>Merge chain ending with residue LEU710 (chain id 'C', atom 4332 OXT) with<br>chain starting with residue CYS145 (chain id 'R', atom 1 N)? [n/y]<br>y<br>Merge chain ending with residue CYS283 (chain id 'R', atom 1400 OXT) with<br>chain starting with residue CYS428 (chain id 'S', atom 1401 N)? [n/y]<br>n<br>Merge chain ending with residue CYS566 (chain id 'S', atom 2800 OXT) with<br>chain starting with residue CYS711 (chain id 'T', atom 2801 N)? [n/y]<br>y<br><br><br><br>*************************<br><br>After ABC , I include a 'TER', then start chain RST, and make 'chainsep ter'<br><br>2. newpdb2gmx -f chainABCRSTter.pdb -p dimertop.top -o dimerpdb.pdb -chainsep ter -ignh<br>Program newpdb2gmx, VERSION 4.5.1<br>Source code file: pdb2gmx.c, line: 655<br><br>Fatal error:<br>Atom OXT in residue LEU 427 was not found in rtp entry LEU with 19 atoms<br>while sorting atoms.<br><br><br>The
residue are not in sequential Order , but i dont think that is the problem here.<br><br>Thank you.<br><br>Best,<br>nahren<br><br><br>--- On <b>Fri, 9/3/10, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] intermolecular distance restrains<br>To: "Gromacs Users' List" <gmx-users@gromacs.org><br>Date: Friday, September 3, 2010, 3:18 AM<br><br><div class="plainMail"><br><br>nahren manuel wrote:<br>> <br>> Dear Gromacs Users,<br>> <br>> 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.<br>> <br><br>How is the .pdb set up? Does it have both chain ID's and TER delimiters? What was your pdb2gmx
command line?<br><br>-Justin<br><br>> I am able to do with -merge in the previous (ver 4.0.7 of ) pdb2gmx.<br>> <br>> Best,<br>> nahren<br>> <br>> --- On *Thu, 9/2/10, Justin A. Lemkul /<<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>>/* wrote:<br>> <br>> <br>> From: Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> Subject: Re: [gmx-users] intermolecular distance restrains<br>> To: "Discussion list for GROMACS users" <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Date: Thursday, September 2, 2010, 8:09 PM<br>> <br>> <br>> <br>> nahren manuel wrote:<br>> > Dear
Gromacs Users,<br>> ><br>> > I am presently using gromacs4.5 beta(since I want implicit<br>> solvent). I<br>> <br>> No need to use a beta version, the official 4.5 has been released.<br>> <br>> > wish to apply intermolecular distance restraints.<br>> > To my surprise there is no merge option in pdb2gmx (although<br>> pdb2gnx -h, says it has). So is there a new alternative to create<br>> intermolecular distance restrains.<br>> ><br>> <br>> Use pdb2gmx -chainsep.<br>> <br>> -Justin<br>> <br>> > Best,<br>> > nahren<br>> ><br>> ><br>> <br>>
-- ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>
</mc/compose?to=<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>> posting!<br>> Please don't post (un)subscribe requests to the list. Use the www<br>> interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> </mc/compose?to=<a ymailto="mailto:gmx-users-request@gromacs.org"
href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>> <br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></blockquote></td></tr></table><br>