[gmx-users] genaral questions

[Sven Huttenhouse]

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?

I increased the distance from 0.1 to 0.52 and it still give me the same 
resigue number. is that normal?

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?
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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