[gmx-users] dealing with ATP

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 23 14:54:58 CEST 2011

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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