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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 25 2022 - 00:30:02 PDT
