回复： Re: [gmx-users] Distance restraints

[xi zhao]

Dear sir : how can you produce distance itp file? Thank you in advance!

Tsjerk Wassenaar <tsjerkw at gmail.com> 写道：  Hi Misha,

You can only apply distance restraints within one molecule, so the workaround is to put the desired SOL molecule in the .itp file (and change the order in the .gro file accordingly).

Hope it helps,

Tsjerk

  On 11/19/05, Иванов Миша <grasp2 at mail.ru> wrote:  
Dear users,

I would like to make a distance restraints. I create a file "disres.itp" with the following content:
[ distance_restraints ]
;  ai    aj    type    index    type    low    up1    up2    fac 
  3177  3906     1        1       1      0.0    0.3    0.7    1
where the first atom is form "chain A" of my system and the second is from "SOL".
My question is:
What command should I untroduce in .top file and in what part of it, to make Grompp understand that the first atom is from CHAIN A and the second - from Solvent. 
My top file is written below.

Sicerely yours,
Misha Ivanov

;       This is your topology file
;       ?
;
; Include forcefield parameters
#include "ffgmx.itp"

; Include chain topologies 
#include "1_A.itp"
#include "1_B.itp"

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

#ifdef POSRES_WATER 
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

[ system ]
; Name
?

[ molecules ] 
; Compound        #mols
Protein_A           1
Protein_B           1
SOL               223



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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB) 
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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