[gmx-users] gmx-user : problem with coordinate number

Nur Syafiqah Abdul Ghani pqah123 at gmail.com
Fri Aug 3 05:51:26 CEST 2012

Dear All,

My project is about protein simulation in mix-solvent.
At first  I used pdb2gmx command then editconf for stting up my box.
My co-solvent I creat it from PRTDRG server to get pdb and itp file.

1. I get the name of the file is DRG.ITP with capital letter.Then i change it
 with new name with small letter but the same type of file.Is it the
capital letter is
affect my file later?

Next, I put genbox -cp protein_box.gro -p topol.top -cs co-solvent.gro
-o protein_solv.gro
The molecule of the co-solvent is added but then i know i to edit the
topology..after that i use the same command but change the -cs with

2. Can i do that?Because when i use -ci -nmol the system freeze and it
kill the programme..

My problem start when i wanted to minimize the protein before adding
ion.I used grompp -f minim_first.mdp -o protein_minimize.tpr -p
topol.top -c protein_mixture.gro
and the output said that

Fatal error:
number of coordinates in coordinate file (protein_mixture.gro, 92850)
             does not match topology (topol.top, 87524)

But i already check both file with instruction from
http://www.gromacs.org/Documentation/Errors but it seems that my file
contain the same amount number of molecules.
I dont know how to solve it.Can anyone suggest to me where the
tutorial for the mix-solvent?

Your kindness help me a lot and i'm grateful that you help me.

Thanks in advance,
Master in Science,
Theoretical and Computational Chemistry,
University Putra Malaysia,

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