RE: problem with angle parameters

From: Radak, Brian K (bradak_at_anl.gov)
Date: Wed Mar 30 2016 - 11:09:12 CDT

It looks like your PSF contains an angle that shouldn't exist. I would examine the connectivity in VMD and verify that your polymer (presumably your own RTF?) is correctly defined.

Regards,
Brian

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov
________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of faride badalkhani [farideh.khamseh_at_gmail.com]
Sent: Wednesday, March 30, 2016 10:01 AM
To: namd-l
Subject: Fwd: namd-l: problem with angle parameters

Dear all

I am setting up a system consists of a polymer in water. When running the NVT simulation I get this error:

UNABLE TO FIND ANGLE PARAMETERS FOR CD OB CD (ATOMS 30 31 30)

while there should not be such angle in my structure. It is only a carbonyl group. Could you help me on that?

Truly yours,
Farideh

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