Thanks for your reply.
I am using Amber 11 and Ambertools 1.4
Best wishes
KS
On Fri, Sep 6, 2013 at 9:04 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> What version of AmberTools are you using?
>
> You could try and see if cpptraj (AmberTools 13) works for you:
>
> cpptraj -p protein.top -y protein_min.crd -x protein_solvent.pdb
>
> -Dan
>
> On Thu, Sep 5, 2013 at 9:25 PM, Krati Sharma <krati84.gmail.com> wrote:
> > Dear Amber user's
> >
> > 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.
> > The real homodimer with a and b chain have the same number of chain and
> the
> > same numbering
> >
> >
> > ATOM 5789 CZ ARG A 728 30.165 64.691 85.588 1.00
> > 82.20 C
> > ATOM 5790 NH1 ARG A 728 31.373 64.164 85.772 1.00
> > 81.01 N
> > ATOM 5791 NH2 ARG A 728 29.094 64.075 86.079 1.00
> > 80.81 N
> > TER 5792 ARG A
> > 728
> > ATOM 5793 N THR B 6 34.101 83.914 30.674 1.00
> > 79.98 N
> > ATOM 5794 CA THR B 6 32.622 83.701 30.563 1.00
> > 80.68 C
> > ATOM 5795 C THR B 6 32.271 82.198 30.415 1.00
> > 80.99 C
> > ATOM 5796 O THR B 6 31.458 81.827 29.552 1.00
> > 82.28 O
> >
> > If you see below the chain is ending at 2163 and the chain b is starting
> > from 2164 instead of 1.
> >
> > ATOM 34303 C ARG 2163 5.387 47.227 -15.222 1.00
> > 0.00
> > ATOM 34304 O ARG 2163 5.611 47.786 -14.144 1.00
> > 0.00
> > ATOM 34305 OXT ARG 2163 5.440 47.901 -16.248 1.00
> > 0.00
> > TER
> > ATOM 34306 N THR 2164 -15.132 51.856 34.718 1.00
> > 0.00
> > ATOM 34307 H1 THR 2164 -14.494 51.092 34.890 1.00
> > 0.00
> > ATOM 34308 H2 THR 2164 -15.462 51.795 33.765 1.00
> > 0.00
> >
> > 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.
> > Does someone has solution to this problem or script to correct the pdb
> > format?
> >
> > Regards
> > *Krati Sharma*
> > *
> >
> > *
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Krati Sharma
Research scholar
UNB (Scfbio*-*IIT)
*
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Received on Fri Sep 06 2013 - 04:00:02 PDT
