On Tue, Oct 31, 2017 at 9:07 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Tue, Oct 31, 2017 at 8:39 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> > On Tue, Oct 31, 2017 at 8:12 AM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >> On Mon, Oct 30, 2017, Hai Nguyen wrote:
> >> >
> >> > the script does work as expected. The index you saw did not reflect
> the
> >> > atom index.
> >>
> >> ?? Does this mean there is no problem? Did you send at17.pdb to tleap?
> >>
> >
> > uhm, I just tried and seems a problem :D.
> >
> > WARNING: There is a bond of 3.114709 angstroms between:
> >
> > ------- .R<CYX 4>.A<SG 8> and .R<CYX 148>.A<CB 5>
> > Removing the CONECT field indeed resolve the case.
>
> If you don't increment the ATOM record number on TER you need to keep
> track of that for the CONECT records, since the latter use ATOM record
> numbers, not actual atom number. CPPTRAJ does this internally so that
> the CONECT records are correct whether you increment on TER or not.
>
I see. Thanks
Hai
> -Dan
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Tue Oct 31 2017 - 06:30:03 PDT
