Thanks!
We were using version 12.4.
We will update our amber tools.
Best regards, Iñigo.
>
> 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 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, Iñigo.
>> _______________________________________________ AMBER mailing list
>> AMBER.ambermd.org [1]
>> http://lists.ambermd.org/mailman/listinfo/amber [2]
> -- ------------------------- 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/
> [4]
> (801) 587-9652 (801) 585-9119 (Fax)
> _______________________________________________ AMBER mailing list
> AMBER.ambermd.org [5] http://lists.ambermd.org/mailman/listinfo/amber
> [6]
> Links:
> ------
> [1] mailto:AMBER.ambermd.org
> [2] http://lists.ambermd.org/mailman/listinfo/amber
> [3] mailto:imarcos.cbm.uam.es
> [4] http://home.chpc.utah.edu/~cheatham/
> [5] mailto:AMBER.ambermd.org
> [6] http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu May 16 2013 - 04:00:03 PDT
