Hello Charles,
If I do not apply the patch, the enery output is usual with no zero
values. I indeed have some warnings, all on this model :
AT_Build::buildNode: cycle link found between atoms 770 LYS 48 C and 774 GLN
49 N
removing bond.
AT_Build::buildNode: cycle link found between atoms 789 GLN 49 C and 791 LEU
50 N
removing bond.
AT_Build::buildNode: cycle link found between atoms 808 LEU 50 C and 810 GLU
51 N
between residues 48 and 71, and only when the patch is applied, it's
probably related, but I do not how.
Thanks for your time,
Olivier
2010/6/23 <Charles at schwieters.org>
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> Hash: SHA1
>
>
> Hello Olivier--
>
> > I have been trying to create an isopeptide bond patch to join two
> > monomers of ubiquitin (Gly76->Lys48) using the amber force field
> > (needed for GB), but the result is that during minimization and
> > dynamics, I have the following output:
> > *--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t=
> 0.001
> > --*
> > | E(kin)+E(poten)= -66.620 E(kin)= 0.689 temperature=
> > 0.971 |
> > | E(poten)= -67.3086349 grad= 0.0000008 ANGL=
> > 0.0000000 |
> > | BOND= 0.0000000 IMPR= 0.0000000 VDW+GBIN+GBSE=
> > -67.3086349 |
> >
> *------------------------------------------------------------------------------*
> >
>
> It's difficult to imagine how the patch could zero out those enery
> terms. Do you get any errors or warnings? Does the same script without a
> patch statement also have the zero energies?
>
> best regards--
> Charles
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