[gmx-users] positional restraint

[Xavier Periole]

Alok wrote:

>
> hello Xavier,
>                    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.
>                                                                        
>                                                                        
>                                        Thanking you
>                                                                        
>                                                                        
>                                           Alok Jain
>
>>
>>> 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
>>
The way you did is ok !! The point was that the atom number for position 
restraints has
to be the one define by the topology number and not the .gro number. Ex: 
the restrain
for water is on the oxygen at number 1, and not define on all oxygen 
atom. For the protein
it works in general because the protein is the first element in the .gro 
so that the
atom number and topology numbers are the same.
In your case may be the confusion comes from the fact that you include 
the PR into the
topology file. The position is the topology file could be the problem.
Try to gmxdump the .tpr file and look for the restrains. look for POSRES 
in the output
and check which atoms are restrained ...

XAvier

-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole
   
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