[gmx-users] dealing with ATP
Justin A. Lemkul
jalemkul at vt.edu
Sat Apr 23 15:16:24 CEST 2011
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
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.
> *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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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