Can you send me the topology and restart files off-list so I can try to
reproduce this error? Thanks.
-Dan
On Friday, September 6, 2013, Krati Sharma wrote:
> Dear Roe
>
> PFA!
>
> 1. Error -try.png
> 2.
> a. This is what in my actual file
> ATOM 11531 CB GLNB 717 47.313 -3.313
> -15.627
> On running tleap, it shows error (try.png)
> FATAL: Atom .R<GL 717>.A<CB 3> does not have a type.
>
> b. When I reduce the gap between ATOM and 11532 (see below) I get
> .top and .crd file
> ATOM 11532 CG GLNB 717 47.822 -1.912 -15.233 (actual file-
> Result in error)
> ATOM 11533 CD GLNB 717 48.945 -1.897 -14.190(edit file- Result in
> .top and .crd generation. Here it reads residue GLN instead just GL)
>
> 3. I tried using -aatm flag and without the same flag................ its
> not helping me to solve this problem
>
> Regards
> Krati Sharma
>
>
> On Fri, Sep 6, 2013 at 5:53 PM, David A Case <case.biomaps.rutgers.edu<javascript:;>
> >wrote:
>
> > On Fri, Sep 06, 2013, Krati Sharma wrote:
> > >
> > > I am generating the solvent file using command
> > > ambpdb -aatm -p protein.top <protein_min.crd> protein_solvent.pdb
> > >
> > > When the protein is lengthy, its causing format problem during tleap
> run.
> > >
> > > If you see below the chain is ending at 2163 and the chain b is
> starting
> > > from 2164 instead of 1.
> >
> > This is expected: the prmtop file that ambpdb is using numbers residues
> > sequentially, not starting over again for each chain.
> >
> > >
> > > ATOM 34303 C ARG 2163 5.387 47.227 -15.222 1.00
> > > ATOM 34304 O ARG 2163 5.611 47.786 -14.144 1.00
> > > ATOM 34305 OXT ARG 2163 5.440 47.901 -16.248 1.00
> > > TER
> > > ATOM 34306 N THR 2164 -15.132 51.856 34.718 1.00
> > > ATOM 34307 H1 THR 2164 -14.494 51.092 34.890 1.00
> > > ATOM 34308 H2 THR 2164 -15.462 51.795 33.765 1.00
> > >
> > > This cause error on running tlesp.If I reduce gap between ATOM and the
> > > number 34303, tleap is reading full residue ARG otherwise it reads RG
> and
> > > causing fatal error.
> >
> > I guess I can't see the problem: the "ARG" string for atom 34303 appears
> > in columns 18-20, as it should. Can you give the exact error message
> from
> > tleap? Can you be more specific about exactly what you did to "reduce
> the
> > gap" between ATOM and the number? (what did the line originally look
> like?
> > what did you change?)
> >
> > Is the result any better if you leave out the -aatm flag? You may be the
> > only
> > person who has used that option in years: it no longer is very useful
> > now that the PDB has gone to the version 3 atom naming scheme. There
> > could be
> > some sort of bug with that flag.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> *Krati Sharma
> Research scholar
> UNB (Scfbio*-*IIT)
>
>
>
> *
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Sep 06 2013 - 08:00:04 PDT
