Dear Mark,
Thank you very much for your help!
I add the restraints into my topol.top successfully!
But there is still two questions:
(1) After [angle_restraints] is added into my .top file, should I write
additional parameters into .mdp file to run
angle restraints? Because after [diheral_restrints] is added to .top
file, extra parameters of dihedral constraint should be added to .mdp
file to function.
(2) Could [position_restraint] and [angle_restraint] be used together
in the same .mdp file? For example, I add position restraints to all the
heavy atoms of my protein, then I add [angle_restraint] to atom
20/22;47/58, is this
reasonable?
Thank you very much!
Best wishes!
Jianing
On 2013-05-18 16:43, Mark Abraham wrote:
On Sat, May 18, 2013 at 10:20 AM, jnsong <jns...@itcs.ecnu.edu.cn>
wrote:
Dear all,
Recently, I want to add angle_restraints and dihedral_restraints for
atoms
in two separate molecules, that is, inter-molecular restraints, not
intra-molecular restraints.
I add the following into my .top file:
[ angle_restraints ]
; i j k l type theta0 fc multiplicity
20 22 47 50 1 0.0 1500 1
[ dihedral_restraints ]
; i j k l type label phi dphi kfac power
25 28 51 52 1 1 180 0 1 2
But it give errors:
"Fatal error:
[ file ang_res.itp, line 5 ]:
Atom index (47) in angle_restraints out of bounds (1-24).
This probably means that you have inserted topology section
"angle_restraints"
in a part belonging to a different molecule than you intended to."
Atom 20/22 belongs to one molecule, and Atom 47/50 belongs to
another
molecule. The same situation is for atom 25/28 and atom 51/52.
I guess this error comes from the fact that I have two separate
molecules
in my simulation system, thus topol_Protein.itp and
topol_Protein2.itp are
produced when using pdb2gmx. Atom 47 in .gro file has atom number 17
in
topol_Protein2.itp. Thus it gives the error that Atom index (47) in
angle_restraints out of bounds!
Additionally, [ angle_restraints] and [dihedral_restraints] seems
for the
intra-molecular interaction definitions.
Would you please tell me how to add angle and dihedral restraints
for the
atoms that belong to two different molecules?
You need both molecules in the same [moleculetype], since the
restraint
directives require this.
pdb2gmx -h will help here.
Mark
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