Mark's suggestion of a hybrid [molecule] section is a good one. Please
note the need to then include disre=simple in your .mdp file. Mark has
previously posted an enhancement request for a grompp warning if you
forget disre=simple in the .mdp file response to some confusion that I
previously had, but I am unsure if this has been incorporated into
v4.0.3.
A currently available alternative is to utilize the pull code (see the
manual).
The requirement that distance restraints be intra-molecular, while
obviously true and seemingly important for .top feasibility based on
separate .itp files, is rather bothersome. Is it not possible,
developers, to include some type of pre-processing that would allow
inter-molecular distance restraints? Perhaps by preprocessing the .top
and .itp files into new files prior to their input to the existing
grompp structure? It seems that this might be easier now that grompp
does not rely on cpp and the grompp preprocessor could now, in theory,
do any type of preprocessing.
Chris.
Pathumwadee Intharathep wrote:
Dear gmx-users,
Do you know how to make distance restraint between ligand and
protein in gromacs?
I have a chain of protein binds with 4 drugs in water-lipid box, the
topology put below..
; File 'top.top' was generated; Include forcefield parameters
;
#include "/home/bio001/02_saow/gromacs_top/jit/top/ffgmx.itp"
#include "/home/bio001/02_saow/gromacs_top/jit/popc.itp"
You can avoid the need to specify particular directories each time
through careful use of the GMXLIB environment variable, or using
"include = -I /some/dir" in your .mdp file. See
http://wiki.gromacs.org/index.php/Include_File_Mechanism
You should also refrain from using ffgmx, as it's been deprecated for
ages now.
; Include chain topologies
#include "1add_H/0H_addH1.top" ;protein atom 1-1615
#include "disre.itp" ; distance
restraint topology file
#include "rimq1_top.itp" ;ligand
topology file atom 1-16
; Include water topology
#include "/home/bio001/02_saow/gromacs_top/jit/top/flexspc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "/home/bio001/02_saow/gromacs_top/jit/top/ions.itp"
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_A 1
RIM 4
POPC 74
SOL 3763
Cl 8
------------------------------------------
detailed in "disre.itp" file is
[ distance_restraints ]
195 1628 1 1 1 0.25 0.35 0.40 1.0
195 563 1 1 1 0.25 0.35 0.40 1.0
598 1644 1 1 1 0.25 0.35 0.40 1.0
598 966 1 1 1 0.25 0.35 0.40 1.0
1001 1660 1 1 1 0.25 0.35 0.40 1.0
1001 369 1 1 1 0.25 0.35 0.40 1.0
1404 1676 1 1 1 0.25 0.35 0.40 1.0
1404 160 1 1 1 0.25 0.35 0.40 1.0
The error occur after grompp run is..
?Fatal error: [ file "../disre.itp", line 2 ]:
Atom index (1628) in distance_restraints out of bounds (1-1615)?
It seems to be that the atoms from ligand (rimq1_top.itp) topology
was not known.
My question is Q1: Where I should put ?disre.itp? in topology file
that it can recognize the atom from both protein (0H_addH1.top) and
ligand (rimq1_top.itp) topology files.
Distance restraints may only be intra-molecular. Thus you will need to
make a hybrid [molecule] section that includes your protein and all of
its distance-restrained ligands and #include "disre.itp" at the end of
that [molecule] section.
Mark
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