[gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?

[ZHANG Cheng]

Hi Mark,


Thank you for your help! Sorry I was totally confused. I thought I should delete the "define = -DPOSRES" option and use "-r target.pdb". Now I understand that.


I should
) still keep the "define = -DPOSRES" in the mdp file
) still keep the "[ position_restraints ]" section in the itp file
) the only difference is, add "-r target.gro" where the "target.gro" can be the same as that for "-c" option.


Thank you very much!


Cheng




------------------ Original ------------------
From:  "ZHANG Cheng"<272699575 at qq.com>;
Date:  Wed, Jan 16, 2019 09:51 PM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;

Subject:  What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?



My understanding is, in the Gromacs 2018, we MUST use "-r target.pdb" to replace the "define = -DPOSRES" option in the .mdp file.


However, how can I do position restraints only for certain atoms, e.g. only the backbone atoms? I think, if I use "-r target.pdb", both the backbone and side chain atoms in the "target.pdb" will be restrained. 




My coarse-grained pdb looks like this:


ATOM      1  BB  PRO A   1     -26.587  30.562  25.782  1.00  0.00           B 
ATOM      2  SC1 PRO A   1     -28.091  28.941  24.961  1.00  0.00           S 
ATOM      3  BB  GLN A   2     -25.999  30.486  29.213  1.00  0.00           B 
ATOM      4  SC1 GLN A   2     -25.071  33.603  31.302  1.00  0.00           S 
ATOM      5  BB  ILE A   3     -23.280  28.735  30.757  1.00  0.00           B 
ATOM      6  SC1 ILE A   3     -23.796  26.273  28.833  1.00  0.00           S 
... ...
ATOM    201  BB  ASN A  98     -16.655  34.258  30.350  1.00  0.00           B 
ATOM    202  SC1 ASN A  98     -18.546  35.721  27.829  1.00  0.00           S 
ATOM    203  BB  PHE A  99     -15.212  36.640  33.153  1.00  0.00           B 
ATOM    204  SC1 PHE A  99     -13.341  34.692  33.167  1.00  0.00           S 
ATOM    205  SC2 PHE A  99     -11.471  35.716  34.112  1.00  0.00           S 
ATOM    206  SC3 PHE A  99     -10.740  34.794  32.402  1.00  0.00           S 







The "position_restraints" looks like this in the protein.itp file: 
(you can see only the backbone atom ID is listed, i.e. 1, 3, 5 ... 201, 203)


#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
 [ position_restraints ]
      1    1    POSRES_FC    POSRES_FC    POSRES_FC
      3    1    POSRES_FC    POSRES_FC    POSRES_FC
      5    1    POSRES_FC    POSRES_FC    POSRES_FC
... ...
    201    1    POSRES_FC    POSRES_FC    POSRES_FC
    203    1    POSRES_FC    POSRES_FC    POSRES_FC
#endif