[gmx-users] positional restraint
alokjain at iitk.ac.in
Thu Nov 25 20:05:28 CET 2004
I am a little confused about this constraint thing
after going through your reply.I would just like to mention the way i
generated my ".itp file" for constraining the residue in my protein.
I initially generated the ".itp file" using pdb2gmx program.The ".itp
file" so generated contained all heavy atoms of my protein with the
corresponding force constant.I then manupulated this ".itp file"
according to my requirements by deleting all atoms expect the heavy
atoms corresponding to my residue of interest.I checked the atom number
of my residue from the ".gro file".
I also wanted to constrain the hydrogen
atoms present in the residue.So I got the the atom number of the
hydrogen atoms present in the residue from the ".gro file" and
consequently added to the ".itp file".So my final ".itp file " contains
only the atom number for all atoms (heavy as well as hydrogens) present
in the residue i want to constrain which i have shown in my first mail.
I then added this ".itp file" to the
".top file" and processed the input files.
Your reply to my previous mail where u have mentioned
"Position restrains have to be assigned on the atom number of the
molecule not the
number in the gro file !!"
has created a doubt if I am doing the right thing for constraining the
residue.Please correct me if I am going wrong.
>> hello gmx uers,
>> I have a problem concerning positional
>> restraint . I am constraining a residue from my protein during
>> minimization and consequently during the early stage of my dynamics.
>> I have consequently constructed an ".itp file" for the purpose of
>> positional restraint of the residue which i then add to the ".top file".
>> The .itp file is as shown below:
>> ; In this topology include file, you will find position restraint
>> ; entries for all the heavy atoms in your original pdb file.
>> ; This means that all the protons which were added by pdb2gmx are
>> ; not restrained.
>> [ position_restraints ]
>> ; atom type fx fy fz
>> 691 1 100000 100000 100000
>> 692 1 100000 100000 100000
>> 693 1 100000 100000 100000
>> 694 1 100000 100000 100000
>> 695 1 100000 100000 100000
>> 696 1 100000 100000 100000
>> 697 1 100000 100000 100000
>> 698 1 100000 100000 100000
>> 699 1 100000 100000 100000
>> 700 1 100000 100000 100000
>> 701 1 100000 100000 100000
>> The output data that i get after preprocessing my input files for
>> minimization is as follows:
>> processing coordinates...
>> double-checking input for internal consistency...
>> Reading position restraint coords from out2sxl.gro
>> renumbering atomtypes...
>> converting bonded parameters...
>> # BONDS: 39330
>> # G96BONDS: 2817
>> # ANGLES: 26220
>> # G96ANGLES: 5464
>> # PDIHS: 2470
>> # IDIHS: 2285
>> # LJ14: 4581
>> # POSRES: 22
> Position restrains have to be assigned on the atom number of the
> molecule not the
> number in the gro file !!
> Just in case you you did not do.
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