Hi JiYuan,
Please send us all the files necessary to reproduce the problem:
3H68_OH_resNames.bcl
3H68_OH_settings.bcl
3H68_OH_params_fc_md.xml
3H68_OH_chg2.xml
3H68_OH_stdMol.xml
3H68_OH_fixed_H.pdb
Regards,
Martin
On 20 Dec 2011, at 02:37, JiYuan Liu wrote:
>
> 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 Tue Dec 20 2011 - 01:30:03 PST
