[gmx-users] dealing with ATP

[Justin A. Lemkul]

Sajad Ahrari wrote:
> 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!?

You're talking about two separate issues - atom types and parameters for 
molecules.  Yes, most (all?) force fields describe both P and S atoms, but I 
guarantee none of them have (by default) parameters for some species named "d" 
that represents ADP-SO4.  You cannot assign parameters from P blindly to S and 
hope for the best.  That sounds fundamentally wrong to me.

In your original message, it sounded like you wanted to change ADP-SO4 into ATP, 
but perhaps I misunderstood what you intended.  No force field will be able to 
assign parameters to ADP-SO4, even though the force field may recognize 
individual atoms, it cannot construct a topology for any arbitrary molecules.

If you need to simulation this ADP-SO4 species, you're in for the long road of 
parameterization:

http://www.gromacs.org/Documentation/How-tos/Parameterization

Otherwise, change the S atom to P and name the molecule ATP so it will be 
recognized by whatever force field you choose, after you have verified that the 
force field can indeed recognize such a species.  Otherwise, you're stuck doing 
parameterization for ATP, too.

-Justin

> regards
> sajad
> 
> ------------------------------------------------------------------------
> *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.
> 
> -Justin
> 
>  > i do appreciate your help!
>  > sajad
>  >
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

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