[gmx-users] gromacs simulation

[Justin A. Lemkul]

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?

-Justin

> Pls give me some suggession.
> 
> Best regards,
> nittopuran
> Bioinformatics..
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> 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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================