If you want, send me the topology and a restart of your system
off-list and I can try to reproduce.
-Dan
On Wed, May 18, 2016 at 12:14 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
> Hi Dan,
> Thanks,
>
> Yes, I am waiting for the implementation of AT16.
> And, yes it’s an amber topology. Anything else does not really work.
>
> Rami
>
> On May 18, 2016, at 2:01 PM, Daniel Roe <daniel.r.roe.gmail.com<mailto:daniel.r.roe.gmail.com>> wrote:
>
> Hi,
>
> First, just to make sure, the topology you are using has charges and
> non-bonded parameters, right? Also, there have been some fixes to the
> 'pairwise' command since AT15. I would recommend upgrading to AT16 and
> trying again.
>
> -Dan
>
> On Wed, May 18, 2016 at 11:47 AM, Osman, Roman <roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>> wrote:
> Hello,
>
> I wrote the list yesterday about problems using the pairwise command in cpptraj (AmberTools15), but did not receive a response.
>
> The following is the message from yesterday.
> Thanks.
> Roman Osman
>
>
> I was wondering whether I am using the pairwise command in cpptraj correctly.
> when I type
>
> pairwise erg2_magea3 :56,59,195 out erg2_magea3_ener.dat eout erg2_magea3_e.dat cuteelec 0.0 cutevdw 0.0
>
> I would like to see the results poer atom but results in the eout file have no values:
>
> PAIRWISE: Frame 0
> PAIRWISE: Cumulative Evdw: Evdw < -0.0000, Evdw > 0.0000
> PAIRWISE: Cumulative Eelec: Eelec < -0.0000, Eelec > 0.0000
> PAIRWISE: Frame 1
> PAIRWISE: Cumulative Evdw: Evdw < -0.0000, Evdw > 0.0000
> PAIRWISE: Cumulative Eelec: Eelec < -0.0000, Eelec > 0.0000
>
> When I add to the command a pdbout statement:
> pairwise erg2_magea3 :56,59,195 out erg2_magea3_ener.dat eout erg2_magea3_e.dat cuteelec 0.0 cutevdw 0.0 pdbout erg2_magea3.pdb
>
> I get this error
>
> Error: [pairwise] Not all arguments handled: [ pdbout erg2_magea3.pdb ]
> 1 errors encountered reading input.
>
> Thanks for your help
>
> Roman Osman
> Department of Structural and Chemical Biology
> Mount Sinai School of Medicine
> New York, NY 10029
> Tel: 212-659-8627
> Fax: 212-849-2456
> e-mail: roman.osman.mssm.edu<mailto:roman.osman.mssm.edu><mailto:roman.osman.mssm.edu>
>
>
>
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>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> https://urldefense.proofpoint.com/v2/url?u=http-3A__home.chpc.utah.edu_-7Echeatham_&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=LxI3LPy_I2wl0EUqkWbdI6JU9Rx_TG35PlL4yBAgQDM&s=O0TPxrA9fnzZ9vvdCnG0UuEj3h3WVVTjdgee8rgQbyo&e=
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>
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> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=AwICAg&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=LxI3LPy_I2wl0EUqkWbdI6JU9Rx_TG35PlL4yBAgQDM&s=NK6hCtL_C4trAgyjW_Np0jP2tlYsrL5tnaqHiFOvcKQ&e=
>
> Roman Osman
> Department of Structural and Chemical Biology
> Mount Sinai School of Medicine
> New York, NY 10029
> Tel: 212-659-8627
> Fax: 212-849-2456
> e-mail: roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed May 18 2016 - 12:00:04 PDT
