On 3/08/2012 1:51 PM, Nur Syafiqah Abdul Ghani wrote:
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?
A lower-case suffix is probably more likely to work.
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
spc216.gro..
2. Can i do that?Because when i use -ci -nmol the system freeze and it
kill the programme..
IIRC genbox needs the solvent to be named SOL and be last in the
[molecules] list. If this behaviour is with GROMACS 4.5.5, please file
an issue at http://redmine.gromacs.org/. There are more effective
workflows, however. Place the non-water molecules first, then use genbox
-cs.
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.
So if [molecules] is accurate with respect to your coordinate file, then
the moleculetype names must not be what you think they are.
I dont know how to solve it.Can anyone suggest to me where the
tutorial for the mix-solvent?
Google knows where they are.
Mark
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