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. I also tried to use cpptraj to strip the prmtop file, but the issue still exsits. Is there any way to let amber not delete Mg ion?
Thank you,
Tao
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Received on Tue Mar 29 2022 - 22:00:02 PDT
