Hi Ji-Yuan,
On 17/11/2011, at 8:54 a.m., Áõ¼ªÔª wrote:
> Hi Ben,
> I am very sorry I found a mistake with 3H68_OH_large.bcl,I wrote a wrong code not bb in the residues that between ACE and NME.It is running very normally now.Thank you.
Huh, serve me right for not reading this email. I guess you can disregard my response. Incidentally, if this kind of thing happens in future, I encourage you to "reply" to your earlier email (while changing the sender so you're sending to the correct person or list). This course of action will keep your emails together in the same thread - very useful for responders who are following a discussion and want to make sure nothing is missed.
> I have an important question: when I created the side chain model by hand,I dont know how to add the parameters of ligand with a small molecule that has three oxygen coordinated with two ZN2+/MN2+ in the *_sidechain.bcl.If I dont add the ligand information in that file. I need your help to solve the problem above.
You will need to do so based on the GAFF force field parameters. Have a look at the files "atomtypes_gaff.xml" and "parm_gaff.xml" under $AMBERHOME/dat/mtkpp.
Hope that helps,
Ben
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Received on Thu Nov 17 2011 - 15:30:04 PST
