[gmx-users] Polar Hydrogen missing using PRODRG

[Justin A. Lemkul]

Jennifer Williams wrote:
> 
> 
> Hi,
> 
> I am trying to get a .itp file for a simple molecule (Ibuprofen). This 
> contains a COOH group.
> 
> THe problem is that PRODRG removes the polar hydrogen of the COOH from 
> the .pdb file and generates a .itp file without it.
> 
> I am not concerned about the other aromatic hydrogens but I really need 
> the polar hydrogen modelled explicitly.
> 
> Is there a fix for this within PRODRG?
> 
> I know I can use pdb2gmx to add hydrogens but the residue names of the 
> pdb file are not recognized by the existing forcefields so I usually 
> bypass using pdb2gmx.
> 
> 

Have a look at the PRODRG FAQ - there's an entry there for modifying protonation 
state.

-Justin

> Thanks
> 
> Jenny
> 
> 
> 
> Dr. Jennifer Williams
> Institute for Materials and Processes
> School of Engineering
> University of Edinburgh
> Sanderson Building
> The King's Buildings
> Mayfield Road
> Edinburgh, EH9 3JL, United Kingdom
> Phone: ++44 (0)131 650 4 861
> 
> 

-- 
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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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