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
--
========================================
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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