look in AmberTools/src/sander/mdread2.F90
carlos
On Wed, Nov 20, 2024 at 10:20 AM Osman, Roman via AMBER <amber.ambermd.org>
wrote:
> Hello,
>
> I am getting a Bad atom type error in MMPBSA
> When I am trying to include a K+ in the ligand, which is charged.
>
> I found this recommended fix in the amber archive:
> http://archive.ambermd.org/201502/0363.html#start
>
> I'm trying to run MMPBSA.py.MPI on a local cluster, and my system contains
> > a K+ that I've added into mdread.F90 as this entry-
> >
> > else if (atype == 'K+') then
> > ! K+ ionic radius is 152 pm to 1.52 angstroms
> > ! See archive.ambermd.org/201101/0220.html for more info
> > x(L165-1+i) = 1.52d0 + 1.4d0
>
> but it’s from 2015 and when I look for the program mdread.F90, I cannot
> find it.
>
> Could someone help with identifying how to fix this in amber24.
> Thanks
>
> Roman Osman
> Professor
> Department of Pharmacological Sciences
> Icahn School of Medicine at Mount Sinai
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 20 2024 - 08:30:06 PST
