Re: FATAL ERROR: Duplicate bond

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Wed Mar 11 2009 - 17:48:13 CDT

Are these atoms part of non-standard topology? Perhaps of a new residue you
have attempted to parameterize or of a "hybrid" residue prepared for FEP
calculations? If so, odds are that in the BONDS section of your top file
you have the bond listed twice. Bonds in top files are listed by pairs of
atom names. If this is the case, deleting one of them and generating a new
psf should fix the problem.

C.

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
Fax: 217-244-6078
JC Gumbart <gumbart_at_ks.uiuc.edu> writes:
> Date: Wed, 11 Mar 2009 17:17:36 -0500
> From: JC Gumbart <gumbart_at_ks.uiuc.edu>
> To: 璀 李 <letitgone1984_at_yahoo.com.cn>
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: FATAL ERROR: Duplicate bond
> Return-Path: char_at_halifax.ks.uiuc.edu
> Message-Id: <7E147C4B-2567-4ED8-9BA0-5A966633E3EE_at_ks.uiuc.edu>
> X-Spam-Status: No, score=-2.4 required=5.0 tests=ALL_TRUSTED,AWL,BAYES_00,
>       HTML_50_60,HTML_IMAGE_ONLY_20,HTML_MESSAGE,HTML_SHORT_LINK_IMG_3
>       autolearn=unavailable version=3.1.7-0+tcb1
>
> You should probably first try to figure out why the extra bond was added
> to begin with - what did you use to build the files?  Modifying the psf
> file directly is an option, but is likely to cause more problems than it
> solves.
>
>
> On Mar 11, 2009, at 2:45 AM, 璀 李 wrote:
>
>> Hi, everyone
>> When I run my program. the error came out that duplicate bond was
>> found between 2 atoms.
>> Reason: FATAL ERROR: Duplicate bond from atom 13429 to atom 13437
>>
>> Charm++ fatal error:
>> FATAL ERROR: Duplicate bond from atom 13429 to atom 13437
>>
>> Should I delete the bond directely? How to do it since my psf file was
>> huge?
>>
>> Thanks
>>
>>
>>    Tracy Lee
>> LMMD
>>   ECUST
>>
>>
>> 好玩贺卡等你发,邮箱贺卡全新上线!
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:36 CST