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.
-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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 31 2017 - 06:30:02 PDT
