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> 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>
>
>
>
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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 - 11:30:04 PDT
