[gmx-users] gromacs simulation

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 16 02:15:14 CEST 2009

Enamul Haque wrote:
> Hello!
> 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,
> nittopuran
> Bioinformatics..
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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