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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Aug 3 06:14:30 CEST 2012

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 

> 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.


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