Hi Agostino,
On 29/03/2012, at 10:08 PM, Agostino Bruno wrote:
> Dear Ben,
>
> attached there are all the files that I used/generated to parametrize my
> ligand. I send all by this mail (out of the mailing list), because of the
> amber mailing list do not allow me to send large mail. For the steric clash I
> checked with vmd using the command
>
> same residue as exwithin 1 of resname 5HE, while for the water and ion
> molecules I am quite convinced that Xleap worked well. I already parametrize
> other systems using Xleap, and I never met this kind of proble.
Hmm. Well, as you suggest, it's not any overlapping atom. I would next suggest that you have a look at the excluded atoms list, by running rdparm on the topology file and executing "printExcluded" (note: not "printExluded", as the help would suggest). See if there are any 1-2 or 1-3 pairs in there that are missing for your residue.
If you think it's the dihedrals that are responsible, one thing you could do to test that theory is to set the parameters for the particular dihedrals you're concerned about to zero, and see if you get any change in the result.
Hope that helps,
Ben
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Received on Thu Mar 29 2012 - 03:00:03 PDT
