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 - 07:30:05 PST
