[gmx-users] genaral questions

[David]

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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