Hi,
Three things:
1. There was a change in the cpin format from amber 18, which affects
cases where you try to titrate "too" many residues at once.
Please re-create your cpin using Amber22 and try again.
2. I would warn you a lot against titrating 72 residues at once. Even if
every residue in your protein was somehow changing protonation states at
the pHs you want, you would need very long MD runs to feel like you
sampled both conformational space AND protonation space.
Think of the following: The regular pKa of an aspartic acid is ~4 and of
a lysine is ~10. What are the chances that you will find a pH where BOTH
of those residue change protonation state under those conditions ? There
are examples where that happens, but they are so rare, that you need a
really good reason to do it, because of the extra computational cost.
So, if you are running this at [H=4 for example, I would not bother with
CYS, TYR, LYS, unless you KNOW something about the system beforehand.
At pH 9, I would not bother with ASP/GLU
In particular, if any of these residues is fully solvent exposed and not
making strong contacts with the protein, I would not try to titrate them.
3. You can titrate CYS and TYR, but they are much less validated than
the other residues. In fact, I have almost never seen a deprotonated
tyrosine, except in VERY particular circumstances.
Our parameters for CYS are not quite right yet, we are almost finished
with a good set, which we will publish when ready.
Adrian
On 10/27/22 1:19 PM, Dulal Mondal via AMBER wrote:
> [External Email]
>
> Dear Users,
> I am running Umbrella Sampling at constant pH. I found the following error.
>
> "At line 233 of file /home/dulal/amber22_src/src/pmemd/src/constantph.F90
> (unit = 23, file = 'amber.cpin')
> Fortran runtime error: Cannot match namelist object name 'residue:"
>
> The cpin file is attached below. I generated the cpin file using amber 18.
> Can any one help me?
>
>
>
>
> With regards,
> Dulal Mondal
>
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--
Dr. Adrian E. Roitberg (he/him/el)
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Oct 27 2022 - 11:30:02 PDT
