[gmx-users] gromacs simulation

Enamul Haque nittopuran at gmail.com
Wed Sep 16 02:07:13 CEST 2009


I am trying to build articaine (local anesthetic) molecular structure with
JME editor. According to  prodrg instruction, All hydrogens should need to
be avoided. But I really dont know how to do that? I have attached a .JPG
file for articaine. I dont know is it the right structure or not? But it
contains hydrogen. I cannot remove the hydrogen from the structure. Would
you pls give me some suggession how to do that?  And when I want to run
genbox command to to add  like 12 articaine molecules to the  DMPC lipid
bilayer it adds 8 or 11 or 9 molecules. Not the exact one. I wonder why this
is happening? Anybody pls give me some suggession!!

The command that I have used to add 12 articaine molecule to the DMPC lipid
bilayer is given below-

genbox -cp dmpc128.gro -ci articaine.gro -o dmpcarti.gro -nmol 12

I have generated the articaine.gro coordinate file with the dundee prodrg
server using the built articaine  . But it add only 8/9 or 10 molecule. Not
the exact 12 molecule.

Pls give me some suggession.

Best regards,
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