[gmx-users] Re: gmx-users Digest, Vol 46, Issue 67
sudheer babu
sudheer.pbm07 at gmail.com
Fri Feb 22 07:07:51 CET 2008
Thank you Mr.justin
On Thu, Feb 21, 2008 at 9:50 PM, <gmx-users-request at gromacs.org> wrote:
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> 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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Problem regarding tc_grps
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1203591740.47bd5a3ca8997 at webmail.vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Quoting sudheer babu <sudheer.pbm07 at gmail.com>:
>
> > 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
> jalemkul at vt.edu | (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" <sudheer.pbm07 at gmail.com>
> Subject: [gmx-users] problem about position restrain
> To: gmx-users at gromacs.org
> Message-ID:
> <76de29310802210403h80bac8bke6ed6a42c5668654 at mail.gmail.com>
> 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
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> ------------------------------
>
> Message: 3
> Date: Thu, 21 Feb 2008 07:27:33 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] problem about position restrain
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1203596853.47bd6e355c11c at webmail.vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Quoting sudheer babu <sudheer.pbm07 at gmail.com>:
>
> > 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
> jalemkul at vt.edu | (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" <ssupakar at gmail.com>
> Subject: [gmx-users] Building Topology with all hydrogens
> To: gmx-users at gromacs.org
> Message-ID:
> <28ab3fc70802210420q65a6a757x78f23b7c30f028c1 at mail.gmail.com>
> 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
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> ------------------------------
>
> Message: 5
> Date: Thu, 21 Feb 2008 08:17:08 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Building Topology with all hydrogens
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1203599828.47bd79d444753 at webmail.vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Quoting Subhrangshu Supakar <ssupakar at gmail.com>:
>
> > 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
> jalemkul at vt.edu | (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 <markus.miettinen at tkk.fi>
> Subject: [gmx-users] Re: T-Coupling and COM removal
> To: gmx-users at gromacs.org
> Message-ID: <9D00BEE0-ECC2-4943-A9F4-7075EF20B0B3 at tkk.fi>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> On Feb 20, 2008, at 19:36 , gmx-users-request at gromacs.org wrote:
>
> > Message: 4
> > Date: Wed, 20 Feb 2008 09:15:33 -0800
> > From: "Ilya Chorny" <ichorny at gmail.com>
> > Subject: [gmx-users] T-Coupling and COM removal
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Message-ID:
> > <5f5f916d0802200915y1beff759ye244b11775355553 at mail.gmail.com>
> > 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" <jalemkul at vt.edu>
> Subject: [gmx-users] CHARMM nonbonded parameters and grompp output
> To: gmx-users at gromacs.org
> Message-ID: <1203610784.47bda4a013ba3 at webmail.vt.edu>
> 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
> 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 46, Issue 67
> *****************************************
>
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