Re: [gmx-users] Restrain specific lipid residues
That's a simple enough way to deal with it - thanks! On Sep 25, 2012, at 2:16 PM, Justin Lemkul wrote: > > > On 9/25/12 5:14 PM, Katrina Lexa wrote: >> Hi everyone, >> >> This is probably a very silly question, but if I want to restrain only >> certain lipid residues in my bilayer, based on their residue number, is >> there some other way to do this aside from just having an explicit >> residue-by-residue list of them & their topologies in my .top? I'm just >> using Tieleman's lipid parameters, so I cannot define the lipid residues to >> restrain following the popc.itp file, since it describes just the general >> topology for any POPC residue & tells me that my index is out of range, >> since the .top is in atom numbers & I'm trying to think in residue numbers. >> Does that sort of make sense? Out of my 165 residues, I want to strongly >> restrain only 33 of them, and then let the rest minimize (I'm trying to add >> onto an equilibrated box - at this point, it would have just been easier to >> start over from scratch, but I thought I would ask). >> > > Restraints can only be applied per [molecultype], so no, there is no way to > have a global lipid topology and individual restraint files for individual > molecules. It is possible to reduce the complexity a bit by defining the 33 > restrained lipids as one [moleculetype], though they would have to be > consecutive in your coordinate file as well, which may require manual > reorganization. > >> Also, thank you to Justin and Mark for your help with hydrogen building in >> pdb2gmx - you were right, obviously, I was just not noticing the wrong atom >> type in my .h2b file (way back Aug 30th). >> > > Glad to hear there's at least one problem solved :) > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Restrain specific lipid residues
Hi everyone, This is probably a very silly question, but if I want to restrain only certain lipid residues in my bilayer, based on their residue number, is there some other way to do this aside from just having an explicit residue-by-residue list of them & their topologies in my .top? I'm just using Tieleman's lipid parameters, so I cannot define the lipid residues to restrain following the popc.itp file, since it describes just the general topology for any POPC residue & tells me that my index is out of range, since the .top is in atom numbers & I'm trying to think in residue numbers. Does that sort of make sense? Out of my 165 residues, I want to strongly restrain only 33 of them, and then let the rest minimize (I'm trying to add onto an equilibrated box - at this point, it would have just been easier to start over from scratch, but I thought I would ask). Also, thank you to Justin and Mark for your help with hydrogen building in pdb2gmx - you were right, obviously, I was just not noticing the wrong atom type in my .h2b file (way back Aug 30th). Thank you for your help, Katrina-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] help with "interaction of type atom in the topology database, but an atom of that name was not found in residue" error
Hello Gromacs Users: I apologize for asking a question that has come up several times in the forum, but I have read the answers to those posts and I am not still unable to fix the error based on the suggestions in the previous emails. It is completely possible that I am just not seeing the obvious, so I apologize, but I would welcome any advice. I just have a methylated glycine that I would like to use (SAR) within a peptide with the AMBER force field, but when I try to build the cyclic compound it writes out: Opening force field file ./amber99sb_lipid.ff/atomtypes.atp Atomtype 1 Reading residue database... (amber99sb_lipid) Opening force field file ./amber99sb_lipid.ff/aminoacids.rtp Residue 100 Sorting it all out... Opening force field file ./amber99sb_lipid.ff/aminoacids.hdb Back Off! I just backed up topol.top to ./#topol.top.59# Processing chain 1 'A' (85 atoms, 11 residues) Identified residue ALA1 as a starting terminus. Identified residue ALA11 as a ending terminus. 9 out of 9 lines of specbond.dat converted successfully Opening force field file ./amber99sb_lipid.ff/aminoacids.arn Checking for duplicate atoms --- Program pdb2gmx, VERSION 4.5.5 Source code file: pgutil.c, line: 91 Fatal error: Atom CB is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 7. However, my residue 7 should not have a CB atom, I'm not seeing it in my pdb file or the .rtp file (impropers section or otherwise). Perhaps that residue is being skipped, but all of my atoms are "ATOM" rather than HETATM, and I don't have any tabs messing up the fields. this is the SAR (residue 7) section in my .rtp file [ SAR ] [ atoms ] NN -0.22670 1 CNCT -0.22340 2 HN1H0.10210 3 HN2H0.10210 4 HN3H0.10210 5 CACT -0.02520 6 HA2H1 0.06980 7 HA3H1 0.06980 8 CC0.59730 9 OO -0.5679010 [ bonds ] NCN NCA CA C CA HA2 CA HA3 CN HN1 CN HN2 CN HN3 C O -C N [ impropers ] -CCA N H CA+N C O and here is a chunk of my pdb file MODEL1 ATOM 1 N ALA A 1 -5.608 1.167 2.062 1.000.00 N1+ ATOM 2 CA ALA A 1 -4.930 0.579 3.183 1.00 0.00 C ATOM 3 CB ALA A 1 -5.857 0.458 4.396 1.00 0.00 C ATOM 4 C ALA A 1 -3.814 1.597 3.525 1.00 0.00 C ATOM 5 O ALA A 1 -4.063 2.822 3.391 1.00 0.00 O ATOM 6 N MLE A 2 -2.575 1.132 3.819 1.00 0.00 N ATOM 7 CN MLE A 2 -2.315 -0.257 4.265 1.00 0.00 C ATOM 8 CA MLE A 2 -1.398 2.052 3.941 1.00 0.00 C ATOM 9 CB MLE A 2 -1.091 2.218 5.462 1.00 0.00 C ATOM 10 CG MLE A 2 -2.145 2.883 6.382 1.00 0.00 C ATOM 11 CD1 MLE A 2 -1.689 2.877 7.897 1.00 0.00 C ATOM 12 CD2 MLE A 2 -2.626 4.302 5.946 1.00 0.00 C ATOM 45 N ABA A 6 4.961 4.195 -6.289 1.00 0.00 N ATOM 46 CA ABA A 6 5.219 4.813 -7.615 1.00 0.00 C ATOM 47 CB ABA A 6 6.627 4.541 -8.037 1.00 0.00 C ATOM 48 CG ABA A 6 7.673 5.523 -7.418 1.00 0.00 C ATOM 49 C ABA A 6 4.374 4.037 -8.636 1.00 0.00 C ATOM 50 O ABA A 6 4.360 2.841 -8.453 1.00 0.00 O ATOM 51 N SAR A 7 3.818 4.705 -9.676 1.00 0.00 N ATOM 52 CN SAR A 7 4.087 6.071 -9.873 1.00 0.00 C ATOM 53 CA SAR A 7 2.929 3.969 -10.548 1.00 0.00 C ATOM 54 C SAR A 7 1.449 4.131 -10.258 1.00 0.00 C ATOM 55 O SAR A 7 0.975 5.236 -10.559 1.00 0.00 O ATOM 56 N MLE A 8 0.814 3.165 -9.517 1.00 0.00 N ATOM 57 CN MLE A 8 1.365 1.822 -9.318 1.00 0.00 C ATOM 58 CA MLE A 8-0.491 3.432 -8.917 1.00 0.00 C ATOM 59 CB MLE A 8-1.599 2.488 -9.538 1.00 0.00 C ATOM 60 CG MLE A 8-2.739 3.173 -10.337 1.00 0.00 C ATOM 61 CD1 MLE A 8-3.758 3.767 -9.396 1.00 0.00 C ATOM 62 CD2 MLE A 8-2.404
