[gmx-users] genaral questions
David
spoel at xray.bmc.uu.se
Thu Nov 10 21:09:28 CET 2005
On Thu, 2005-11-10 at 13:50 -0600, Sven Huttenhouse wrote:
> Dear Dr. David
> thank you for your help.
> I checked the charges in the top file and I got the following:
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB
> chargeB massB
> 1 opls_287 1 GLY N 1 -0.3 14.0067 ; qtot
> -0.3
> 2 opls_290 1 GLY H1 1 0.33 1.008 ; qtot
> 0.03
> 3 opls_290 1 GLY H2 1 0.33 1.008 ; qtot
> 0.36
> 4 opls_290 1 GLY H3 1 0.33 1.008 ; qtot
> 0.69
> 5 opls_298 1 GLY CA 1 0.09 12.011 ; qtot
> 0.78
> 6 opls_140 1 GLY HA1 1 0.06 1.008 ; qtot
> 0.84
> 7 opls_140 1 GLY HA2 1 0.06 1.008 ; qtot
> 0.9
> 8 opls_271 1 GLY C 2 0.7 12.011 ;
> qtot 1.6
> 9 opls_272 1 GLY O1 2 -0.8 15.9994 ; qtot
> 0.8
> 10 opls_272 1 GLY O2 2 -0.8 15.9994 ; qtot
> 0
> the some of the charges is not -1 nor 1 in both groups. can I consider this
> a zwitterion?
Yes.
> I increased the distance from 0.1 to 0.52 and it still give me the same
> resigue number. is that normal?
There is no relation between the two.
>
> I ususally change the number of glycine molecules to 200 immediatly after I
> generate the .gro, .top and .itp files from the origenal .pdb file but I
> give the topology file a different name like the origenal file has the name
> glyc.top and the modified file named 200glyc.top is this ok?
Yes.
> I use this file in the genbox and it work fine.
>
> thank you again for your reply.
>
> kind regards
> Sven
>
> >From: David <spoel at xray.bmc.uu.se>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] genaral questions
> >Date: Thu, 10 Nov 2005 20:25:55 +0100
> >
> >On Thu, 2005-11-10 at 13:04 -0600, Sven Huttenhouse wrote:
> > > Dear all
> > > I'm trying do a MD simulation for glycine crystallization. I have a pdb
> >file
> > > for glycine and I converted it to a .pdb file for zwitterion using
> >pdb2gmx
> > > program as follow:
> > > pdb2gmx -f glyc.pdb -o zwitglyc.pdb -inter
> > > I chosed force field 3 and zwitterion glycine NH3+ and COO-
> > > I reviewed the topology file for the zwitterion but it didn't show a
> >charge
> > > of -1 on the Oxygen atom nor +1 on the Nitrogene.
> >The charges are spread out over the NH3 and COO, check the total charge
> >in the comment on the right.
> >
> > >
> > > **Is that normal? and how will I make sure that I gor a zwitterion?**
> > >
> > > I then generated a .gro, .top and .itp files from the zwitterion file
> >using
> > > pdb2gmx as follow:
> > > pdb2gmx -f zwitglyc.pdb -o zwitglyc.gro -p zwitglyc.top -i zwitglyc.itp
> > > -inter
> > > I then chosed force field 3 and zwitterion glycine NH3+ and COO-. I then
> > > generated 200 molecules from thr .gro file I have using genconf as
> >follow:
> > > genconf -f zwitglyc.gro -o 200zwitglyc.gro -nbox 5 5 8 -dist 0.1 0.1 0.1
> >Dist 0.1 is good only if the original box is large enough, otherwise
> >increase it.
> >
> > > I got 200 separated molecules but with the same residue number.
> >Perfect. Now go to your topol.top file and change protein from 1 to 200.
> > >
> > > **How can I make sure that gromacs consider them separate molecules? and
> >how
> > > can I generate molecules with different resodue numbers?**
> >DOn't worry this will be fine after EM or MD.
> >
> > >
> > > I then thought It will be better if I generate 200 molecules in a .pdb
> >file
> > > and I did so using genconf but again I got separate molecules with the
> >same
> > > residue number (200zwitglyc.pdb).
> >Don't do it. Follow recipe above.
> >
> > > I tried to use this file to generate the .gro, .top and .itp files for
> >200
> > > molecules usinf pdb2gmx as follow:
> > > pdb2gmx -f 200zwitglyc.pdb -o 200zwitglyc.gro -p 200zwitglyc.top -i
> > > 200zwitglyc.itp -inter
> > > but I got files that contain one molecule only.
> > >
> > > ** why did I get files with one molecule although they were generated
> >from a
> > > file containing 200 molecules?**
> >Since pdb2gmx thinks it is a single chain. If you had 200 different
> >chain labels in the file (impossible) then it might work.
> > >
> > > it will be great if someone can help me.
> > >
> > > Kind regards
> > > Sven
> > >
> > > _________________________________________________________________
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> >--
> >David.
> >________________________________________________________________________
> >David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> >Dept. of Cell and Molecular Biology, Uppsala University.
> >Husargatan 3, Box 596, 75124 Uppsala, Sweden
> >phone: 46 18 471 4205 fax: 46 18 511 755
> >spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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