[gmx-users] Three molecules in single topol.top file

SAKO MIRZAIE sako.biochem at gmail.com
Wed Aug 31 23:24:18 CEST 2016


Dear Jang,

it seems that some of angles in your topology file are not defined in
bonded interaction. you can check angle constructed by atom 1    3
2 in your topology file.


On 8/31/16, Chang Woon Jang <changwoonjang at gmail.com> wrote:
> Dear Mark Abraham,
>
>     I am a little confused about the meaning of "you have not taught grompp
> how to handle" (especially *taught*) because I have topology file,
> conf.gro, nonbonded and bonded force fields, grompp.mdp, index file. Do I
> need to do something else in order to specify the interaction?
>
>     What I have done is 1) reduced time-step, 2) check the initial
> configuration because the CG system actually is mapped from equilibrated
> atomistic system, 3) using -rdd options, 4) extend table-extension value.
> None of them works.
>
>     Would you give me any comments?
>
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
>
> On Wed, Aug 31, 2016 at 12:31 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> There's no need to use separate itp files.the include mechanism just
>> pastes
>> it back in.
>>
>> The actual error message shows you have an interaction that you have not
>> taught grompp how to handle. Investigate that.
>>
>> Mark
>>
>> On Wed, 31 Aug 2016 18:12 Nikhil Maroli <scinikhil at gmail.com> wrote:
>>
>> > It is impossible to make any comments without knowing the simulation
>> > details. I hope it will help , if not provide the full details
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>> > gmx-tutorials/complex/02_topology.html
>> > --
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>
>
> --
> Best regards,
> Changwoon Jang,
>
> Postdoctoral Research Fellow
> Department of Chemical & Biological Engineering, Drexel University
> 3141 Chestnut Street, Philadelphia, PA 19104
>
> Voice: (662) 617-2267
> E-mail: cj395 at drexel.edu
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-- 
***********************************************
Sako Mirzaie
PhD in biochemistry, Assistant Professor, science faculty, Islamic
Azad university of
Sanandaj, Sanandaj, Iran

http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie

http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie

http://scholar.google.com/citations?user=viwZvVAAAAAJ&hl=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
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