[gmx-users] genbox generating acetonitrile box with holes

[Justin A. Lemkul]

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
> 
> #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.
>  

How does the unmodified "protin_in_acetonitrile.gro" look?

> 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.
> 

It would be far simpler to just post an image online, i.e. bullet point #4 here:

http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette

-Justin

> Thanks in advance.
> 
> Diana
> 
> -- 
> Diana Lousa
> PhD student
> Protein Modeling Laboratory
> ITQB/UNL
> Oeiras, Portugal
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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