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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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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Received on Wed May 18 2016 - 11:30:05 PDT
