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)?
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?
Thanks,
Sadegh
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Received on Tue Mar 21 2017 - 13:00:02 PDT
