Thank you Mr.justin On Thu, Feb 21, 2008 at 9:50 PM, <[EMAIL PROTECTED]> wrote:
> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > > You can reach the person managing the list at > [EMAIL PROTECTED] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: Problem regarding tc_grps (Justin A. Lemkul) > 2. problem about position restrain (sudheer babu) > 3. Re: problem about position restrain (Justin A. Lemkul) > 4. Building Topology with all hydrogens (Subhrangshu Supakar) > 5. Re: Building Topology with all hydrogens (Justin A. Lemkul) > 6. Re: T-Coupling and COM removal (Markus Miettinen) > 7. CHARMM nonbonded parameters and grompp output (Justin A. Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Feb 2008 06:02:20 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Problem regarding tc_grps > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1 > > Quoting sudheer babu <[EMAIL PROTECTED]>: > > > Dear gmx-users, > > I am working on membrane proteins, I have done position restrain step > > successfully but, I have doubt about that tc_grps how to use? I have > > searched in gmx-archives regrading this problem , but I found > controversial > > answers like 1.tc_grps - protein sol Cl > > 2. > > tc_grps - protein sol_Cl > > 3. > > tc_grps - protein Non-protein > > And, from the archives, you have undoubtedly seen many responses about > which to > use. Also have a look at: > > http://wiki.gromacs.org/index.php/Thermostats > > -Justin > > > Thanks in advance. > > > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > > > ------------------------------ > > Message: 2 > Date: Thu, 21 Feb 2008 17:33:47 +0530 > From: "sudheer babu" <[EMAIL PROTECTED]> > Subject: [gmx-users] problem about position restrain > To: gmx-users@gromacs.org > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi gmx users, > I am trying to run position restrain step for protein embedded in popc. is > it possible to do position restrain at a time for both popc and protein > like > below mentioned here? > in " .top " file > ; Include Position restraint file > #ifdef POSRES > #include "lip_posre.itp" > #include "posre.itp" > #endif > > or any other way to do position restrain for both. > pls help me..... > Thanks in advance > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080221/b671efd0/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 21 Feb 2008 07:27:33 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] problem about position restrain > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1 > > Quoting sudheer babu <[EMAIL PROTECTED]>: > > > Hi gmx users, > > I am trying to run position restrain step for protein embedded in popc. > is > > it possible to do position restrain at a time for both popc and protein > like > > below mentioned here? > > in " .top " file > > ; Include Position restraint file > > #ifdef POSRES > > #include "lip_posre.itp" > > #include "posre.itp" > > #endif > > I don't know, have you tried it? Does it seem to work? Something that I > have > done before is the following: > > ; position restrain protein > #ifdef POSRES > #include posre.itp > #endif > > ; position restrain lipid > #ifdef POSRES_LIPID > #include lipid_posre.itp > #endif > > That way, you can define both, or only one throughout the course of > minimization > and equilibration, i.e.: > > define = -DPOSRES -DPOSRES_LIPID > > or > > define = -DPOSRES > > -Justin > > > > > or any other way to do position restrain for both. > > pls help me..... > > Thanks in advance > > > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > > > ------------------------------ > > Message: 4 > Date: Thu, 21 Feb 2008 17:50:14 +0530 > From: "Subhrangshu Supakar" <[EMAIL PROTECTED]> > Subject: [gmx-users] Building Topology with all hydrogens > To: gmx-users@gromacs.org > Message-ID: > <[EMAIL PROTECTED]> > Content-Type: text/plain; charset="iso-8859-1" > > Hi All ! > I want to do a MD study of a few molecules in a box of sodium cetyl > sulphate. > I want the the topology Sod-cetyl-sulphate with all its hydrogens as > without > that there would occur a mismatch > in the number of atoms in the system and the number of atoms in the > topology > file. I tried the the dundee server, but I got the topology of the > molecule > with no H. > Can any one suggest a possible way for building the topology for the > Sod-cetyl-sulphate with all its hydrogens. > > Subhrangshu Supakar > Dept. of Bioinformatics > WestBengal University of Technology > Kolkkata, India > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20080221/f13b546e/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Thu, 21 Feb 2008 08:17:08 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Building Topology with all hydrogens > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1 > > Quoting Subhrangshu Supakar <[EMAIL PROTECTED]>: > > > Hi All ! > > I want to do a MD study of a few molecules in a box of sodium cetyl > > sulphate. > > I want the the topology Sod-cetyl-sulphate with all its hydrogens as > without > > that there would occur a mismatch > > in the number of atoms in the system and the number of atoms in the > topology > > file. I tried the the dundee server, but I got the topology of the > molecule > > with no H. > > Can any one suggest a possible way for building the topology for the > > Sod-cetyl-sulphate with all its hydrogens. > > You will have to derive the parameters yourself. See relevant discussions > about > ligands, drugs, etc. in the list archive (this sort of thing has been > asked > dozens of times in recent memory). Also have a look at: > > http://wiki.gromacs.org/index.php/Parameterization > > http://wiki.gromacs.org/index.php/Exotic_Species > > -Justin > > > > > Subhrangshu Supakar > > Dept. of Bioinformatics > > WestBengal University of Technology > > Kolkkata, India > > > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > > > ------------------------------ > > Message: 6 > Date: Thu, 21 Feb 2008 15:42:54 +0200 > From: Markus Miettinen <[EMAIL PROTECTED]> > Subject: [gmx-users] Re: T-Coupling and COM removal > To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > On Feb 20, 2008, at 19:36 , [EMAIL PROTECTED] wrote: > > > Message: 4 > > Date: Wed, 20 Feb 2008 09:15:33 -0800 > > From: "Ilya Chorny" <[EMAIL PROTECTED]> > > Subject: [gmx-users] T-Coupling and COM removal > > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > > Message-ID: > > <[EMAIL PROTECTED]> > > Content-Type: text/plain; charset="iso-8859-1" > > > > HI All, > > > > I ran some membrane protein simulations and got some strange > > results. The > > RMSD (~.18 nm) of the protein equilibrated quite nicely but when I > > look at > > the trajectory the protein seems to be diffusing way to much over > > 20ns. The > > protein has about 1000 AA. I calculated the KE of the protein, > > lipid, and > > water and got a KE that was 1.5RT, 1.2RT, and .8RT respectively. > > My T is > > 298K. > > My COM removal and T-coupling is for the whole system. I am running > > 3.3.1. > > Is there a problem with T-coupling and COM removal on the whole > > system? > > If you have set nstcomm=1, you should not experience a drift. > > For some reason, however, the center of mass of the whole simulation > can slowly drift, even if explicit removal (nstcomm = 1) has been set. > A Bugzilla has been posted, please see > > http://bugzilla.gromacs.org/show_bug.cgi?id=165 > > for further details. > > > Cheers, > Markus Miettinen > > > ------------------------------ > > Message: 7 > Date: Thu, 21 Feb 2008 11:19:44 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: [gmx-users] CHARMM nonbonded parameters and grompp output > To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1 > > > Hi all, > > As a number of others have attempted, I am exploring the use of the CHARMM > force > fields in Gromacs. I have read about a number of difficulties throughout > the > list archive, but I am seeing something that thusfar it seems no one has > reported, regarding nonbonded parameters. Let me tell you what I've done > so > far, and perhaps someone can shed some light on what's going on. > > I downloaded the ffcharmm* files from the old User Contribution site, > following > a link I found in the archive. I created a .hdb file (for ease of use) > and > edited the .tdb files, as they contained some inconsistencies in atom > naming > and formatting. I converted the CHARMM27 force field parameters from Alex > MacKerell's site using a script that was also made available through User > Contributions, giving me ffcharmm.itp, ffcharmmbon.itp, and ffcharmmnb.itp. > So > far, so good. For the moment, I am also approximating the Urey-Bradley > potential by using distance restraints, using scripts that came along with > the > ffcharmm package. > > I was able to produce a topology for hen egg white lysozyme (a decent > system to > test, I thought), with correct disulfides, charges, etc. and life was > good. I > ran grompp to attempt an in vacuo energy minimization, and saw this among > my > output: > > processing topology... > Generated 0 of the 8646 non-bonded parameter combinations > > The rest of the grompp output indicated no errors or warnings (aside from > a net > charge, which is OK for now). I reasoned that there should be _some_ form > of > nonbonded interactions within the protein, correct? I read about 1-4 > interactions (i.e. OPLSAA generates these by scaling, so they are not > explicitly included in ffoplsaanb.itp), but such scaling is reportedly not > used > in the CHARMM force field, and thus it was no surprise to find [ > nonbond_params > ] within ffcharmmnb.itp. This brings me to my question: is grompp not > finding > these parameters? And if so, why? > > I noticed that ffcharmmnb.itp is formatted much like the GROMOS force > field > files (ffgmxnb.itp, ffG*nb.itp) and saw something that is not mentioned in > the > manual. The first line under [ atomtypes ] in each of the GROMOS force > fields > has formatting like: > > ;name at.num mass charge ptype c6 c12 > O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06 > > The at. num column is not mentioned in the manual (Gromacs version 3.3). > Is it > needed for proper interpretation of the *nb.itp files? Such a column is > missing in my ffcharmmnb.itp file. The [ nonbond_params ] and [ pairtypes > ] > sections seem to have correct formatting, so I am not sure that this > (potential) inconsistency among the [ atomtypes ] is causing the issue. > > Thanks for reading (yet another) long email from me, and thanks in advance > if > anyone has any ideas as to what's going on. > > -Justin > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 46, Issue 67 > ***************************************** >
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