[gmx-users] positional restraint

[Alok]

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
>
>
>
> 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.
> XAvier
>