[gmx-users] positional restraint
alokjain at iitk.ac.in
Fri Nov 26 19:08:27 CET 2004
thank you for your reply.I checked my ".tpr file"
using gmxdump.The number reported in the output for POSRES is not the
number of atoms restrained.Also I checked that the atoms restrained are
the ones from my residue.So i am now clear that the required atoms from
my residue are selected for restrain.
I have a small query to make about the value of force
constant.I tried using 1000.I then checked the distances between the
constrained atoms after energy minimization and found considerable
change in the distances between the atoms.I then increased it to
1000000,the distance difference has reduced but still the distance
between some atoms has changed quite a bit.
I also tried to constrain my whole protein
and changed the force contant values from 1000 to 1000000 and cheked the
animation (using ngmx),I still find considerable movement for my protein.
Though i have increased the force
constant value,I am not sure about the detrimental structural effect ( I
have read somewher that too large the force constant may result in
structural artifacts) it may have on my protein.So I would like to know
about the ideal value for the force constant such that the atoms are
constrained considerably and also that the protein does not experience
any unwanted structural deformation.
Xavier Periole wrote:
> 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 ...
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