On Tue, 21 Mar 2017 15:50:28 -0400
Sadegh Faramarzi Ganjabad <safaramarziganjabad.mix.wvu.edu> wrote:
> Dear all,
>
> I am working TI tutorial out to calculate pKa of ionizable residues.
> I had two questions about it;
>
> 1) Say we start with a protonated residue and eliminate the proton
> gradually with changing lambda from 1 to 0, as is noted in TI
> tutorial. The clambda specified in the input file seems to be generic
>
> http://ambermd.org/tutorials/advanced/tutorial6/files/model_step2.mdin
>
> how do we specify that the clambda only applies to a part of peptide
> that changes during ionization (H and itsadjacent atoms)?
With pmemd you would need to use timask1/2 (see manual). Sander does
not have this as it would consider all atoms as "common" atoms. I
assume the vanishing hydrogen atom is of OH/oh atoms type with zero vdW
parameters. If that atoms has those parameters than look into scmask.
> 2) I have two MD trajectories for a protein with protonated and
> deprotonated glutamic acid. Simulations are run with AMBER, but the
> parameters and topology are taken from CHARMM ff (we used chamber
> tool to convert them to AMBER prmtop). I want to use a final
> structure form one of them, for example the protonated one and do a
> TI calculation on it without changing parameters (except
> redistributing charges on deprotonated carbonyl group of course). In
> the tutorial, AMBER ff is used to assign new charges:
>
> http://ambermd.org/tutorials/advanced/tutorial6/files/create_ash.leaprc
>
>
> I am wondering if there is a way to do this step without using AMBER
> ff?
The TI code in sander/pmemd doesn't support the CHARMM force field.
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Received on Tue Mar 21 2017 - 14:00:03 PDT
