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
Received on Thu Sep 05 2013 - 21:00:02 PDT
