Hi Ben,
My e-mail client seems to be creating new threads all the time?It may be
misunderstanded me,I still reply my the email since you reminded me at the
first time.No more than I would like to delete the first "Re:" and only
remain one "Re:"in the title of every replyï¼it could cause to create new
threads?If yes,I am so sorry.
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
toadd fragments like CH3 to my small molecule?
I will arrange all the BCL scripts to you in the next reply.
Best Regards
JiYuan
-------- åå§é®ä»¶ --------
å件人: Ben Roberts <ben.roberts.geek.nz>
åéæ¶é´: 2011-11-29 23:10
æ¶ä»¶äºº: AMBER Mailing List <amber.ambermd.org>
主ãé¢: Re:Re: [AMBER] How MCPB add ligand
withasmallmoleculein*_siderchain.bcl
Hi JiYuan,
On 28/11/2011, at 10:47 p.m., JiYuan Liu wrote:
>
> 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.
First, a mailing list tip for you. Somehow your e-mail client seems to be
creating new threads all the time, even if you "Reply". Disabling that
behaviour would be good; you could then keep the entire discussion in a
single thread, rather than splitting it up into multiple threads that are
very difficult for others to follow if they should have the same problem.
Second, addressing your main point. That seems like a lot of trouble to go
to, and I agree that it shouldn't be necessary. However, I still don't have
enough of your input files to properly test the functioning of the program
and see what needs to be changed in your BCL script (or if there really is a
problem that must be fixed in the source code). In addition to the BCL and
PDB files you sent (thank you), we will also need any files that are sourced
in your BCL script (like 3H68_OH_settings.bcl), files that are sourced in
those files (if any), files that are sourced in files sourced in those files
(if any), and so on.
Regards,
Ben
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Received on Tue Nov 29 2011 - 09:30:03 PST
