[gmx-users] gromacs simulation
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 16 02:15:14 CEST 2009
Enamul Haque wrote:
> 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!!
IIRC, the PRODRG information is warning you that the topology generated
corresponds to a united-atom force field, and thus you should not attempt to use
the topology with an all-atom structure.
Also realize that the charges and charge groups produced by PRODRG are often
unsatisfactory, requiring manual alteration, as well as thorough validation.
> 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.
Is there sufficient space in the bilayer coordinate file to fit in 12 molecules?
> Pls give me some suggession.
> Best regards,
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users