[gmx-users] genaral questions

[Sven Huttenhouse]

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.

**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
I got 200 separated molecules but with the same residue number.

**How can I make sure that gromacs consider them separate molecules? and how 
can I generate molecules with different resodue numbers?**

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).
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?**

it will be great if someone can help me.

Kind regards
Sven

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