[gmx-users] Re: gmx-users Digest, Vol 97, Issue 185
rethina malliga
sgrm.bu at gmail.com
Fri May 25 09:19:48 CEST 2012
On Thu, May 24, 2012 at 12:49 PM, <gmx-users-request at gromacs.org> wrote:
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> 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.sena at gmail.com>
> Subject: [gmx-users] Tabulated potential 1-4 interactions
> To: gmx-users at gromacs.org
> Message-ID:
> <CAGbPF0VZ5U0YBUxRBn3yhLM20enYxUxAcioLBPALC6CcLsEOpQ at 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
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> ------------------------------
>
> Message: 2
> Date: Thu, 24 May 2012 07:49:11 +0200
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] ptn ptn interaction
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FBDCBD7.2090006 at 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 <ramadavidgroup at gmail.com>
> Subject: Re: [gmx-users] Justin umbrella sampling tutorial......
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <CAD=-SYG208+tCnGCmM3ZQpQ_ZU_9DEFnd_eNhK1_U_xKHOFjEw at 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
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> ------------------------------
>
> Message: 4
> Date: Thu, 24 May 2012 12:07:01 +0530
> From: vivek sharma <viveksharma.iitb at gmail.com>
> Subject: [gmx-users] Re: Regarding error.
> To: Seera Suryanarayana <palusoori at gmail.com>
> Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAAU9zysNqFaFVxcqyhLXdvejikovb1b_PGQg=autJzZmK=BTMg at 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 <palusoori at 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.
> >
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> ------------------------------
>
> Message: 5
> Date: Thu, 24 May 2012 00:18:22 -0700 (PDT)
> From: Kowsar Bagherzadeh <kw_bagherzadeh at yahoo.com>
> Subject: Re: [gmx-users] g_rms -bm
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> <1337843902.36526.YahooMailNeo at web161506.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Justin
>
> Thank you very muchh
>
> Sogol
>
>
> ________________________________
> From: Justin A. Lemkul <jalemkul at vt.edu>
> To: Kowsar Bagherzadeh <kw_bagherzadeh at yahoo.com>; Discussion list for
> GROMACS users <gmx-users at 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
>
> ========================================
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> End of gmx-users Digest, Vol 97, Issue 185
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>
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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