Hi,
Yes... if 1UBQ-CG is the coordinates you want the restraints to target.
Mark
On Mon, Jan 14, 2019 at 3:49 PM ZHANG Cheng <272699...@qq.com> wrote:
> Thank you Mark!
>
>
> The "Protein_A.itp" is obtained by:
> python martinize.py -f 1UBQ.pdb -o single-ubq.top -x 1UBQ-CG.pdb -dssp
>
Thank you Mark!
The "Protein_A.itp" is obtained by:
python martinize.py -f 1UBQ.pdb -o single-ubq.top -x 1UBQ-CG.pdb -dssp
./dssp-2.0.4-linux-amd64 -p backbone -ff martini22
So the "Protein_A.itp" has the restraints in the "1UBQ-CG.pdb".
So I should use "-r 1UBQ-CG.pdb"?
So the whole
To add to Mark's comments, it's commonly the case that you want to apply
restraints based on the starting configuration, e.g. for restraining
protein positions at the beginning of a run. As the warning message says,
you can pass the same file to both -c and -r for these cases.
Also, you're
Hi,
The purpose of applying position restraints is to restrain the coordinates
to a set of target coordinates. grompp now requires you to be explicit
about what target you choose. You need to decide what they are, and pass
the file containing them to grompp -r.
Mark
On Mon, Jan 14, 2019 at 3:17
Thank you Mark!
Sorry, I do not have a "targetcoords.gro" for the grompp.
I was trying to use
"gmx grompp -p system.top -c solvated.gro -f minimization.mdp -o
minimization.tpr",
and the "system.top" has a line of " #include "Protein_A.itp" ",
and the "Protein_A.itp" file has the restraints I
Hi,
On Mon, Jan 14, 2019 at 2:54 PM ZHANG Cheng <272699...@qq.com> wrote:
> My backbone restraints is shown in the "Protein_A.itp" file:
>
>
>
> #ifdef POSRES
> #ifndef POSRES_FC
> #define POSRES_FC 1000.00
> #endif
> [ position_restraints ]
> 11POSRES_FCPOSRES_FCPOSRES_FC
My backbone restraints is shown in the "Protein_A.itp" file:
#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
11POSRES_FCPOSRES_FCPOSRES_FC
31POSRES_FCPOSRES_FCPOSRES_FC
51POSRES_FCPOSRES_FC
