Thanks Jason!
As I've noticed pdb2pqr server have assigned exactly such names to the
titrable residues. The only issue id sue to the some problems with some
hydrogen types added by the server to my pdb
FATAL: Atom .R<NSER 64>.A<H 14> does not have a type.
FATAL: Atom .R<CYM 112>.A<HN 11> does not have a type.
FATAL: Atom .R<CYM 218>.A<HN 11> does not have a type.
Does it possible to ignore all hydrogens presented in the processed in
such pdb allowing leap to add it to the structure again?
TFH,
James
2014-06-03 19:59 GMT+02:00 Jason Swails <jason.swails.gmail.com>:
> On Tue, Jun 3, 2014 at 1:44 PM, James Starlight <jmsstarlight.gmail.com>
> wrote:
>
> > Dear Amber users!
> >
> > I'd like to assign protonation states of the titrable residues of my
> > protein using proPKa server and make further parametrization of its
> outtput
> > pdb consisted of protein with hydrogens using some of the amber parameter
> > sets keeping all hydrogens and protonation states predicted by ProPKa.
> I've
> > tried to do such task using amber99sb ff but some residues like
> > deprotonated CYS have not been recognized by that param set.
>
>
> ​Deprotonated CYS is available in ff99SB (as well as ff12SB and ff14SB).
> You have to rename the residue CYM instead of CYS (CYX is for cysteines
> involved in a disulfide bond). Among the various residues that Amber
> provides with different protonation states:
>
> ASP - deprotonated aspartate
> GLU - deprotonated histidine
> CYS - protonated cysteine
> LYS - protonated lysine (+1 total charge)
> HIS/HIE - histidine protonated at N-epsilon
> HID - histidine protonated at N-delta
> HIP - histidine protonated at both N-epsilon and N-delta
> ASH - protonated aspartic acid
> GLH - protonated glutamic acid​
> CYM - deprotonated cysteine
> LYN - deprotonated (neutral) lysine
>
> The trick in all cases to change the protonation state is to change the
> residue name in the PDB to the residue name Amber recognizes as the
> "correct" protonation state (correct in the sense that is the protonation
> state you want to model).
>
> If one is not on this list (like deprotonated tyrosine), you will have to
> derive charges and create a library file for that residue (or find one that
> someone else has created already).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Jun 04 2014 - 07:00:02 PDT
