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 <[EMAIL PROTECTED]> 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
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