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

[Mark Abraham]

Hi,

Nothing has changed in the implementation. Atoms which have interactions
specified have always had get position coordinates to target from
somewhere. (Those atoms with no position restraint interactions never
cared.) Historically the position coordinates came from the file you used
for -c if you didn't use -r. Now you have to use -r, and you can give it
the same file as for -c if you want the old behavior. That's what the
grompp message says, right?

Mark

On Wed., 16 Jan. 2019, 14:52 ZHANG Cheng, <272699575 at qq.com> wrote:

> 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
> --
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