[gmx-users] genbox generating acetonitrile box with holes

[Diana Lousa]

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.

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101105/f0aa675b/attachment.html>