Re: [AMBER] mmpbsa divalent ion bug

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 2 Apr 2022 08:26:16 -0400

You need to specify a custom strip_mask that does not delete the atom you want to keep.

--
Jason M. Swails 
> On Mar 25, 2022, at 3:27 AM, xiangyu <t21714030.stu.ahu.edu.cn> wrote:
> 
> Hello amber users，
> I think there may be a bug when amber dealing with striped prmtop files during running of mmpbsa.py.  In my system there are one protein and two ligands:  ligand 2(GDP), and a Mg2+, together with protein are considered as Receptor. Ligand 1 is defined as ligand.  I correctly formed stripped prmtops using ante-MMPBSA.py -p Cmp.prmtop -c Cmp_vac.prmtop -s :WAT,Na+ -r Rec_vac.prmtop -m @1-2682,@2760-2799 -l Lig_vac.prmtop   But when running mmpbsa.py, it forms wrong inpcrd file(_MMPBSA_dummycomplex.inpcrd) corresponding to the Cmp_vac.prmtop. The Mg2+ ion is automatically removed in the inpcrd causing the 'NATOM mismatch in coord and topology files' error.  Is there any way to let amber not delete Mg ion? 
> 
> 
> Thank you,
> Tao
> 
> 
> 
> 
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Received on Sat Apr 02 2022 - 05:30:02 PDT