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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Mar 20, 2012, at 7:19 PM, George Tzotzos <gtzotzos.me.com> wrote: > HI Jason, > > Numerically, they seem to be way out. Disulfide bonds are ~2 Å. Tleap has a cutoff of 2.2Å (see AmberTools "disulfcut"). I was wondering if it is appropriate to use - if possible at all - tleap to adjust the bond length to this cutoff distance. But even if it were, wouldn't this create "distortions" elsewhere? > > As I mentioned earlier the starting structure was generated by homology modelling. > > Thanking you for your suggestions > > George > > On Mar 21, 2012, at 12:01 AM, Jason Swails wrote: > >> On Tue, Mar 20, 2012 at 2:30 PM, George Tzotzos <gtzotzos.me.com> wrote: >> >>> Hi everybody, >>> >>> In building a topology file, I get the following disulfide bond warnings: >>> >>> Checking Unit. >>> WARNING: There is a bond of 3.493686 angstroms between: >>> ------- .R<CYX 19>.A<SG 8> and .R<CYX 54>.A<SG 8> >>> WARNING: There is a bond of 3.201259 angstroms between: >>> ------- .R<CYX 50>.A<SG 8> and .R<CYX 108>.A<SG 8> >>> WARNING: There is a bond of 3.240445 angstroms between: >>> ------- .R<CYX 97>.A<SG 8> and .R<CYX 117>.A<SG 8> >>> WARNING: The unperturbed charge of the unit: -8.998000 is not zero. >>> >>> Is it safe to disregards them? >>> >> >> Are any of them unexpected to you? (Visualizing is typically very helpful >> with this) >> >> If they are not unexpected, these are fine. >> >> HTH, >> Jason >> >> >>> >>> Note that the original pdb file was built by means of homology modelling. >>> >>> Many thanks for any suggestions >>> >>> George >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >> >> >> >> -- >> Jason M. Swails >> Quantum Theory Project, >> University of Florida >> Ph.D. Candidate >> 352-392-4032 >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Mar 20 2012 - 19:00:03 PDT