(unknown charset) Re: [AMBER] MTK++ and MCPB patch released

From: (unknown charset) JiYuan Liu <liujiyuan.nwsuaf.edu.cn>
Date: Tue, 20 Dec 2011 10:37:27 +0800

   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
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