回复： Re: [gmx-users] Distance restraints

[David van der Spoel]

xi zhao wrote:
> Dear sir : how can you produce distance itp file? Thank you in advance!
1. manually (ch. 5)
2. using src/contrib/xplor2gmx.pl (from exp. data)

> 
> */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 <mailto: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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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