[gmx-users] regarding the positional restraints

[aneesh chandran]

helllo Mark
 Thank you for your quick reply.
 i have already checked what ever you just told but even then i am getting this problem 
 Sir 
 i would be very thankful if you could tell me any other options like what are the files one should look  for resolving this type of restraint problem
 
 i have checked in the archive also but  i did not find any related question.
 
 Thanks 
 following is my input file 
 
    cpp           = /lib/cpp   ; Preprocessor
    define        = -DPOSRE
    integrator    = steep
    emtol         = 100        
   nsteps        = 500        
   nstenergy     = 50         
   nstxtcout     = 50         
   xtc_grps      = Protein    
   energygrps    = Protein     
   nstlist       = 5          
   ns_type       = simple     
   rlist         = 1.0        
   coulombtype   = PME        
   rcoulomb      = 1.0        
   rvdw          = 1.0        
   constraints   = none       
   pbc           = no         
 following is the part of psore.itp file :
  position restraints for Protein-H of Protein
 
 [ position_restraints ]
 ;  i funct       fcx        fcy        fcz
   13    1         50         50         50
   15    1         50         50         50
   16    1         50         50         50
   17    1         50         50         50
   18    1         50         50         50
   19    1         50         50         50
   20    1         50         50         50
   21    1         50         50         50
   23    1         50         50         50
 
 following is the part of topology file :
 ; Include Position restraint file
 #ifdef POSRES
 #include "posre.itp"
 #endif
 
 Thanks 
 With regards
 Aneesh cna 
 
 
  

Mark Abraham <Mark.Abraham at anu.edu.au> wrote: aneesh chandran wrote:
> Hello Users
> 
> I am using gromacs 3.3 with g43a1 force field.
> 
> I ran a minimization using  some positional restraints.
> For that i used Define = -dposre in the input file but inspite of that 
> on checking the log file for the output i found that there is no energy 
> term corresponding to the positional restraints. also i can see much 
> deviation in the protein structure also.
> 
> I have checked all the required files but did not find any problem in them.
> i am having a proper posre.itp file in the directory
> 
> What else should i check to rectify this problem?
> waiting for an early reply

Computers are literal. Follow the examples and conserve upper and lower 
case. See 
http://www.gromacs.org/documentation/reference/online/mdp_opt.html#pp 
and http://wiki.gromacs.org/index.php/Include_File_Mechanism

Mark
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


       
---------------------------------
 5, 50, 500, 5000. Store N number of mails in your inbox. Click here.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070724/5afb6237/attachment.html>