Dan,
Thanks for the offer. Turns out I was using AT14.
I tested it in AT15 and all looks fine.
My apologies for bothering the list.
Rami
On May 18, 2016, at 2:43 PM, Daniel Roe <daniel.r.roe.gmail.com<mailto:daniel.r.roe.gmail.com>> wrote:
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<mailto: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><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><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><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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--
-------------------------
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=AwIGaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=80h8gfWnXRd-mXPSrw98JBRjhncHe1Sopk2U91C1sZg&m=29yT7qgNjGTOAuhJditydASZJfYmW5LvFVvOpN49ebI&s=mxNbogR3ucyhv4QnbhZIhtNt7Rch1qtOWTR83sPopb4&e=
(801) 587-9652
(801) 585-6208 (Fax)
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Roman Osman
Professor of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
(212) 659-8627
roman.osman.mssm.edu<mailto:
roman.osman.mssm.edu>
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Received on Thu May 19 2016 - 07:30:03 PDT
