[gmx-users] genbox generating acetonitrile box with holes

[Mark Abraham]

On 6/11/2010 12:54 AM, Diana Lousa wrote:
>
> Dear all,
>
> I tried to send this message earlier, but I had attached a pdb file 
> and apparently it exceeded the size allowed in the mailing list and is 
> awinting for the list moderator to evaluate it. I apologize if the 
> message is sent twice.
> I am trying to solvate a protein in a box of acetonitrile using 
> genbox. My initial solvent box is a cubic box containing 300 molecules 
> of acetonitrile that has been equilibrated for 500 ps at constant P and T.
>
> I used the following protocol to generate the box:
>
> #######################################################################################
> #create the box
> editconf -f protein.pdb -d 1.2 -o protein_in_box.pdb  -bt dodecahedron
>
> #solvate
> genbox -cp protein_in_box.pdb -cs acetonitrile_eq.gro -o 
> protein_in_acetonitrile.gro
>

If you want to visualize a coordinate file, and you need a .pdb file for 
the purpose, simply write protein_in_acetonitrile.pdb in the above 
command. GROMACS rarely cares what coordinate file format you use, but 
its default is .gro format. See 
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file. 


I've no idea whether the empty.mdp machinations below do work, but if 
they do, then I'd regard the fact that they do as evidence that GROMACS 
has a bug.

> #convert the box to visualize it
> touch empty.mdp
>
> grompp -f empty.mdp  -c protein_in_acetonitrile.gro  -p 
> 01_make_top/protein_ACN.top
>
> trjconv -f protein_in_acetonitrile.gro -o protein_in_acetonitrile.pdb 
> -pbc atom   -ur compact <<EOF
> 0
> EOF
> #######################################################################################
>
> After these steps I get a box that has holes and I can't understand  why.

Do you know what trjconv -h says about -ur compact? Does this explain 
your "holes"?

Mark

> I couldn't send the final pdb file in attachment, if anyone thinks 
> he/she can help and whishes to see the pdb file I will send it to your 
> email.
>
> Thanks in advance.
>
> Diana
>
> -- 
> Diana Lousa
> PhD student
> Protein Modeling Laboratory
> ITQB/UNL
> Oeiras, Portugal
>