On Thu, May 24, 2012 at 12:49 PM, <gmx-users-requ...@gromacs.org> wrote:
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Tabulated potential 1-4 interactions (mohan maruthi sena) > 2. Re: ptn ptn interaction (Justin A. Lemkul) > 3. Re: Justin umbrella sampling tutorial...... (rama david) > 4. Re: Regarding error. (vivek sharma) > 5. Re: g_rms -bm (Kowsar Bagherzadeh) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 24 May 2012 11:46:34 +0600 > From: mohan maruthi sena <maruthi.s...@gmail.com> > Subject: [gmx-users] Tabulated potential 1-4 interactions > To: gmx-users@gromacs.org > Message-ID: > <cagbpf0vz5u0ybuxrbn3yhlm20enyxuxaciolbpalc6cclse...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I am using tabulated potential option for non bonded > interactions. The system that i am using contains on CA(alpha) CB(beta) > ,atoms connected, If i use option > energygrps = CA CB > energytable = CA CA CB CB it caluclates potential > between CA CA and CB CB , CA CB. I also want to use tabulated potential for > 1,4 atoms but this option does not take care of that, so how can i mention > that option in mdp file so that it uses tabulated potential for 1,4 > interaction also. > > Thanks in advance, > > > Regards, > Mohan > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120524/c64863c9/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 24 May 2012 07:49:11 +0200 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] ptn ptn interaction > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4fbdcbd7.2090...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 5/24/12 7:43 AM, rethina malliga wrote: > > Hi, > > > > I tried protein protein simulation in gromacs. > > > > I prepared one ptn and kept seperately with its .top, .itp, .gro files. > > > > Then I prepared another protein and I build the complex of pasting the > .gro file > > of first processed protein in the .gro file of second processed ptn. > > > > In the topol.top of second protein I included the molecule type at the > bottom > > and inserted > > ;Include ligand topology > > #include "posre.itp" > > > > Be careful about name clashes here - the first protein (by default) will > have a > file named "posre.itp" that will be applied to it. If you use the same > name for > different files, you'll probably get other errors. I find it useful to > call > everything based on specific names, like "posre_proteinA.itp" or something > similar. > > > And i run succeccfully the newbox generation, solvent adding commands. > > > > But with the ions adding command it shows fatal error that the atoms in > > topol.top and solv.gro is different. > > > > `Fatal error: > > number of coordinates in coordinate file (solv.gro, 231262) > > does not match topology (topol.top, 237548) > > > > on analysing the difference between two files i come to know that it is > taking > > the atoms of first protein for the second protein though i named first > and > > second proteins different. > > > > After you added the second protein, did you correctly update the > [molecules] > section of the topology? > > > I changed the residue information in .gro of first file to 1LIG and > change > > everything regarding second molecules name as 1LIG > > > > Unless your protein residues are all called LIG, then this is not > appropriate. > > > and after retrying the ions adding command it says no such molecule type > found. > > > > `Fatal error: > > No such moleculetype 1LIG > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > This comes from incorrect naming. Updating [molecules] correctly with the > name > of your second protein [moleculetype] will solve it. Make sure you make > changes > to both the coordinate file and topology at all steps - they should always > match. > > -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 > > ======================================== > > > ------------------------------ > > Message: 3 > Date: Thu, 24 May 2012 11:49:07 +0530 > From: rama david <ramadavidgr...@gmail.com> > Subject: Re: [gmx-users] Justin umbrella sampling tutorial...... > To: jalem...@vt.edu, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: > <CAD=-syg208+tcngcmm3zqpq_zu_9defnd_enhk1_u_xkhof...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Thank you for your reply, > > I am asking you again same question, EXTREMELY SORRY for my stupidity, > > In step six , I unable to differentiate npt and production run by > mdp file as usualy we find difference by define term, > > I think I get meaning upto reason why to use -DPOSRES_B, > but I want to know if we are using same mdp file in both condition > means the npt equilibriation is as same as md production , > > Then why to do npt, just run production md with DPOSRES_B > > > With my best Wishes , > Rama David > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120524/31c75c36/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Thu, 24 May 2012 12:07:01 +0530 > From: vivek sharma <viveksharma.i...@gmail.com> > Subject: [gmx-users] Re: Regarding error. > To: Seera Suryanarayana <paluso...@gmail.com> > Cc: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CAAU9zysNqFaFVxcqyhLXdvejikovb1b_PGQg=autJzZmK=b...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Suryanarayana, > > This error itself tells you that the particular residue 'DAL' is not > available in the residue topology database of the force field you are using > for your simulation. You can check that by yourself in the *.rtp file of > corresponding force field. > The way out of this situation is to build a topology file(*.top/*.itp) for > particular residue/molecule 'DAL' by yourself (you can use topology > generators like topolbuild, PRODRG server etc for the same) and include it > with your molecule topology file. > > You can find more details about the error at > " > > http://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database > ". > > Also, put your queries in gromacs mailing list which will help other users > and increase the chances of getting better solutions. > > Good luck with the simulation, > ~Vivek > > On 24 May 2012 11:55, Seera Suryanarayana <paluso...@gmail.com> wrote: > > > Dear Vivek, > > While running gromacs software i am getting following > > error. > > > > Fatal error: > > Residue 'DAL' not found in residue topology database. > > > > I am new for MD and in particular using of gromacs. Kindly tell me how to > > over come error which is i mentioned above. > > > > > > Suryanarayana Seera, > > PhD student, > > Hyderabad, > > India. > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120524/3a676e37/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Thu, 24 May 2012 00:18:22 -0700 (PDT) > From: Kowsar Bagherzadeh <kw_bagherza...@yahoo.com> > Subject: Re: [gmx-users] g_rms -bm > To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Message-ID: > <1337843902.36526.yahoomail...@web161506.mail.bf1.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Dear Justin > > Thank you very muchh > > Sogol > > > ________________________________ > From: Justin A. Lemkul <jalem...@vt.edu> > To: Kowsar Bagherzadeh <kw_bagherza...@yahoo.com>; Discussion list for > GROMACS users <gmx-users@gromacs.org> > Sent: Thursday, May 24, 2012 9:59 AM > Subject: Re: [gmx-users] g_rms -bm > > > > On 5/24/12 7:24 AM, Kowsar Bagherzadeh wrote: > > > > > > Dear Users, > > I am trying to analyze a ligand-protein simulation results. I read in > the manual > > that using g_rms command with –bm option produces a matrix of average > bond angle > > deviations. And only bonds between atoms in the comparison groups are > > considered. Does it mean that it is for the bonds and their angles that > are > > already in existence? (Not the ones that may be formed throughout > simulation, I > > mean the ligand may for example interact with residues through H-bonds) > .I have > > In this context, a "bond" means an actual chemical bond. A hydrogen bond > is a nonbonded interaction. > > > made a group in my index file named Active site (including only the > active site > > residues), and I have a LIG group as well. If I choose these two groups > for > > g_rms with this command: > > /g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx**/ > > Does it show me how the ligand affects the active site residues bond > angles? > > Potentially. > > > And one more question, how can I study the ligand orientation in the > active site? > > That depends on how you define orientation - internal metrics like > dihedrals or angles between planes of groups in the ligand, relative > measurements like its position with respect to protein residues, etc. All > analysis tools are listed in the manual, Chapter 8 and Appendix D. It's > quite a lot to read, but you'll be able to identify all the various things > you can analyze and how the information might be connected across different > analysis routines. > > -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 > > ======================================== > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120524/aec28145/attachment.html > > ------------------------------ > > -- > 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/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 97, Issue 185 > ****************************************** > Hi Justin, I tried again with correct namings. If I leave the original name for second protein molecule type (Protein_chain_A) unaltered it shows difference in atoms of topol.top and solv.gro. If I alter the molecule type, where ever its instance appears it shows molecule type not found. Thanks in advance -- Regards, Rethina. Rethina Malliga Gunasekaran, Department Of BioInformatics, Science Block, Alagappa University, Karaikudi – 630 003, India. http://alagappauniversity.academia.edu/RethinamalligaGunasekaran/ **
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