[gmx-users] Re: gmx-users Digest, Vol 13, Issue 26

[Anil Kumar]

Dear Anton,

Thanks for your suggestion,i have tried that one.
I have added that entry "define = -DDIS_REST" but still my problem did not
get sort out.
Can you suggest some other way to do this,

regards,
Anil
ANIL KUMAR(Research Scholar)
Bio-Organic Lab No-336(2nd Floor)
Dept. of Chemistry,
I.I.T.Bombay,Powai,
Mumbai-400076 (INDIA)
Ph. No.-022-25764780(Lab),
        022-25764168(Lab)
Fax No:-022-25767152
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> Today's Topics:
>    2. Re: How to fix four different atoms of diffrent residue	in
>       tetrahedral geometry while MD. (Anton Feenstra)
> ------------------------------
>
> Message: 2
> Date: Wed, 11 May 2005 13:20:10 +0200
> From: Anton Feenstra <feenstra at few.vu.nl>
> Subject: Re: [gmx-users] How to fix four different atoms of diffrent
> 	residue	in tetrahedral geometry while MD.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4281EA6A.7060107 at few.vu.nl>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> Anil Kumar wrote:
>
>> Hi,
>>
>> I wnat to do MD of 16mer polypeptide with fixed  tetrahedral geometry of
>> four different atoms of four different residue.
>>
>> I donot understand how to give distance restrain to fix these four
>> atoms.
>>
>> I tried dis_rest.itp
>>
>> [distance_restraints file]
>> ; ai    aj      type    index   type'   low     up1     up2     fac
>> 22      61      1       0       1       0.310   0.335   0.345   1
>> 22      109     1       1       1       0.310   0.335   0.345   1
>> 22      148     1       1       1       0.310   0.335   0.345   1
>> 61      109     1       1       1       0.310   0.335   0.345   1
>> 61      148     1       1       1       0.310   0.335   0.345   1
>> 109     148     1       1       1       0.310   0.335   0.345   1
>>
>> I have included this in corresponding top file.
>>
>> ; Include Position restraint file
>> #ifdef DIS_REST
>> #include "dis_rest.itp"
>> #endif
>
> You will have to say 'defines = -DDIS_REST' in your .mdp file.
>
>
> --
> Groetjes,
>
> Anton
>
> * NOTE: New Phone & Fax numbers (below) *
>
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
> |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
> |             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
> |_____________|_______________________________________________________|
>
>
>
> ------------------------------



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