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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