Hi Ben,
I have updated MTK++ and MCPB patch released,but the situation changed
more worse,so I recoveried my Amber11 and ambertools11.
By the way,I have attached all of files in the maillist with the title "The
charge is wrong when the ligand together with the large model in MCPB",you
could help me to test it,I want to know 3 things which I can not solve.
1. a command findMetalCenters in 3H68_OH_resNames.bcl,when I run this BCL
script,I can' t get the complete bond informations between atom to atom in
3H68_OH.leaprc;
2. in 3H68_OH_resNames.bcl,I checked one of the results with
3H68_OH_mcpb.pdb,it can't Write pdb with new residue names,the residues
which are coordinated with ZN ions could not be change their original name
into the new name as HD1 AS1 et al.
You can refer to these from my attachments.
3. When I runed the min.in with the parmtop that be generated by MCPB, the
two ZN ions is stable after the minimization, but the ligand is deformed
very serious.
I was very warried about these errors,please help me,thank you.
Best Regards
JiYuan
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Received on Mon Dec 19 2011 - 19:00:02 PST
