Hi Ben,
I have found that the H3 torsion or angle is not correct in the small
molecule when I runed *_addHs.bcl.I tried to change the torsion of H3 in the
lib XML of the small molecule,in fact nothing has improved.Could I need to
add fragments like CH3 to my small molecule?
This is my solution now:In my original PDB file,the small molecule is not
add H.I cutted the coordinates of the small molecule from the original
PDB,and save as a PDB file.I used the software as sybyl to add H to the
small molecule,then I also cutted these new coordinates of the small
molecule to replace which located in the original PDB file.Finally made the
newest PDB file of the complex to be a fixed PDB file that will be used in
BCL scripts.
This can make everything normally,but I dont know whether this solution
is reasonable.Please give me some advise.Thank you.
Best Regards
JiYuan
-------- åå§é®ä»¶ --------
å件人: Ben Roberts <ben.roberts.geek.nz>
åéæ¶é´: 2011-11-29 07:16
æ¶ä»¶äºº: AMBER Mailing List <amber.ambermd.org>
主ãé¢: Re:Re: [AMBER] How MCPB add ligand
withasmallmoleculein*_siderchain.bcl
On 28/11/2011, at 12:34 p.m., JiYuan Liu wrote:
>
> Hi Bené
> Could you suggest me to change the torsion value in 93
line(addFragment
> terminal/CH3 bd /NAME/CLR/AN1-6/.CB. ag /NAME/CLR/AN1-6/.CG. tr
> /NAME/CLR/AN1-6/.ND2 131.0),the torsion 131.0 is not reasonable in this
> line?Please give me the detail.
I don't fully understand your question, but I'm confident that you're
capable of changing the torsion angles by yourself. If necessary, try
stepping through increments of 15 degrees and see which torsion angle or
angles produce chemically sensible output.
Ben
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Received on Mon Nov 28 2011 - 20:00:03 PST
