[gmx-users] dealing with ATP

Sajad Ahrari sajadahrari at yahoo.com
Sat Apr 23 15:08:37 CEST 2011

tnx for your help Justin!
but shouldn't the topology of S atom be described for gromacs? unless gromacs 
may know P atom with the same topology as S. although they may not be the same!?

From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sat, April 23, 2011 5:54:58 AM
Subject: Re: [gmx-users] dealing with ATP

Sajad Ahrari wrote:
> Dear users
> i am working with a protein witch holds a hetero-atom in it's pdb structure. 
>the hetero-atom  is named "d" and stands for "ADP+SO4" (in fact the third 
>phosphate of ATP is being substituted with SO4). i wanted to know if gromacs 
>holds a feature to change "d" into ATP? and if so do 

No, but you can use a text editor to replace the S atom with P.

> i need to introduce ATP for Gromacs or it is known for the program?

Some force fields support ATP, some do not.  Check the .rtp files and see what 
you find.


> i do appreciate your help!
> sajad

-- ========================================

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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