AMBER Archive (2009)

Subject: Re: [AMBER] RE: AMBER: xleap problem

From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Wed Jan 07 2009 - 07:34:43 CST

Dear David,

Thank you for the inputs. But xleap is not showing error for these residues
ie 3212,313 etc. it shows the error only for residue 246,247,248,249.

Bala

On Wed, Jan 7, 2009 at 2:06 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Wed, Jan 07, 2009, Bala subramanian wrote:
> >
> > I tried by removing the chain name as you suggested but its giving some
> > other errors. I have attached the pdb file.
>
> Your file has residues with alternate conformations, for example:
>
> ATOM 1252 N AGLY G 312 84.519-139.106 176.817 0.50130.34
> ATOM 1253 N BGLY G 312 84.580-139.093 176.821 0.50130.54
> ATOM 1254 CA AGLY G 312 84.745-138.635 178.168 0.50130.62
> ATOM 1255 CA BGLY G 312 84.870-138.668 178.175 0.50132.03
> ATOM 1256 C AGLY G 312 83.667-137.629 178.521 0.50130.49
> ATOM 1257 C BGLY G 312 84.057-137.472 178.615 0.50132.56
> ATOM 1258 O AGLY G 312 83.395-136.719 177.734 0.50129.55
> ATOM 1259 O BGLY G 312 83.971-136.469 177.901 0.50132.01
> ATOM 1260 N APRO G 313 83.028-137.767 179.695 0.50130.44
> ATOM 1261 N BPRO G 313 83.443-137.553 179.805 0.50133.04
> ATOM 1262 CA APRO G 313 81.972-136.840 180.115 0.50131.53
> ATOM 1263 CA BPRO G 313 82.628-136.463 180.344 0.50134.04
> ATOM 1264 C APRO G 313 82.413-135.375 180.098 0.50132.66
> ATOM 1265 C BPRO G 313 83.434-135.170 180.483 0.50134.58
> ATOM 1266 O APRO G 313 81.581-134.468 180.030 0.50132.16
> ATOM 1267 O BPRO G 313 84.184-134.985 181.445 0.50133.93
> ATOM 1268 CB APRO G 313 81.618-137.333 181.522 0.50130.68
> ATOM 1269 CB BPRO G 313 82.148-137.021 181.686 0.50133.44
> ATOM 1270 CG APRO G 313 82.890-137.969 181.999 0.50130.40
> ATOM 1271 CG BPRO G 313 83.237-137.955 182.081 0.50133.35
> ...
>
> The "A" and "B" designations before the residue name indicate that the
> crystallographic refinement found two locations for these atoms. You
> need to choose the one you want, and edit the pdb file to remove the
> un-wanted conformers.
>
> ...dac
>
>
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