Hi,
What version of cpptraj are you using? In the latest version (13) the
atom index behavior matches that of ptraj:
ATOM 218 N NHE X 13 3.690 6.391 -7.216 1.00 0.00 N
ATOM 219 HN1 NHE X 13 4.562 6.844 -6.978 1.00 0.00 H
ATOM 220 HN2 NHE X 13 2.780 6.591 -6.826 1.00 0.00 H
TER 221 NHE X 13
ATOM 221 O WAT X 14 2.408 -11.996 7.298 1.00 0.00 O
ATOM 222 H1 WAT X 14 2.852 -11.888 6.457 1.00 0.00 H
ATOM 223 H2 WAT X 14 2.186 -11.105 7.568 1.00 0.00 H
-Dan
On Tue, May 14, 2013 at 7:33 AM, imarcos <imarcos.cbm.uam.es> wrote:
> Dear Amber users,
>
> we have been creating some pdb files using cpptraj and ptraj and we
> have obtained an unexpected behaviour with cpptraj TER lines placement.
>
> While ptraj introduces TER lines with the following format:
>
> ATOM 9654 O WAT 606 34.075 42.652 49.927 0.00 0.00
> ATOM 9655 H1 WAT 606 34.847 42.090 49.986 0.00 0.00
> ATOM 9656 H2 WAT 606 34.145 43.065 49.067 0.00 0.00
> TER 0 0
> ATOM 9657 O WAT 607 56.460 89.789 45.998 0.00 0.00
> ATOM 9658 H1 WAT 607 56.244 89.005 46.503 0.00 0.00
> ATOM 9659 H2 WAT 607 56.470 89.492 45.088 0.00 0.00
>
>
> cpptraj creates the following:
>
> ATOM 9661 O WAT 606 34.075 42.652 49.927 0.00 0.00
> ATOM 9662 H1 WAT 606 34.847 42.090 49.986 0.00 0.00
> ATOM 9663 H2 WAT 606 34.145 43.065 49.067 0.00 0.00
> TER 9664 WAT 606
> ATOM 9665 O WAT 607 56.460 89.789 45.998 0.00 0.00
> ATOM 9666 H1 WAT 607 56.244 89.005 46.503 0.00 0.00
> ATOM 9667 H2 WAT 607 56.470 89.492 45.088 0.00 0.00
>
>
> The problem is that the cpptraj format changes the atom index of the
> atoms that follow a TER line and this may complicate further work using
> this pdb file.
>
> Is there anyway to keep using cpptraj while keeping the classic ptraj
> TER line placement?
>
>
> Best regards,
>
> Iņigo.
>
> _______________________________________________
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> 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)
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Received on Tue May 14 2013 - 07:30:02 PDT
