helllo Mark<br> Thank you for your quick reply.<br> i have already checked what ever you just told but even then i am getting this problem <br> Sir <br> 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<br> <br> i have checked in the archive also but i did not find any related question.<br> <br> Thanks <br> following is my input file <br> <br> cpp = /lib/cpp ; Preprocessor<br> define = -DPOSRE<br> integrator = steep<br> emtol = 100 <br> nsteps = 500 <br> nstenergy =
50 <br> nstxtcout = 50 <br> xtc_grps = Protein <br> energygrps = Protein <br> nstlist = 5 <br> ns_type = simple <br> rlist = 1.0 <br> coulombtype = PME <br> rcoulomb = 1.0 <br> rvdw = 1.0 <br> constraints =
none <br> pbc = no <br> following is the part of psore.itp file :<br> position restraints for Protein-H of Protein<br> <br> [ position_restraints ]<br> ; i funct fcx fcy fcz<br> 13 1 50 50 50<br> 15 1 50 50 50<br> 16 1 50
50 50<br> 17 1 50 50 50<br> 18 1 50 50 50<br> 19 1 50 50 50<br> 20 1 50 50 50<br> 21 1 50 50
50<br> 23 1 50 50 50<br> <br> following is the part of topology file :<br> ; Include Position restraint file<br> #ifdef POSRES<br> #include "posre.itp"<br> #endif<br> <br> Thanks <br> With regards<br> Aneesh cna <br> <br> <br> <br><br><b><i>Mark Abraham <Mark.Abraham@anu.edu.au></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> aneesh chandran wrote:<br>> Hello Users<br>> <br>> I am using gromacs 3.3 with g43a1 force field.<br>> <br>> I ran a minimization using some positional restraints.<br>> For that i used Define = -dposre in the input file but inspite of that <br>> on checking the log file for the output i found that there is no energy <br>> term corresponding to the positional restraints.
also i can see much <br>> deviation in the protein structure also.<br>> <br>> I have checked all the required files but did not find any problem in them.<br>> i am having a proper posre.itp file in the directory<br>> <br>> What else should i check to rectify this problem?<br>> waiting for an early reply<br><br>Computers are literal. Follow the examples and conserve upper and lower <br>case. See <br>http://www.gromacs.org/documentation/reference/online/mdp_opt.html#pp <br>and http://wiki.gromacs.org/index.php/Include_File_Mechanism<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list email@example.com<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to firstname.lastname@example.org.<br>Can't post? Read
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