[gmx-users] is there extra parameters in .mdp file for running successful angle_restraints?
jnsong at itcs.ecnu.edu.cn
Tue May 21 11:31:17 CEST 2013
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
Thank you very much!
On 2013-05-18 16:43, Mark Abraham wrote:
> On Sat, May 18, 2013 at 10:20 AM, jnsong <jnsong at itcs.ecnu.edu.cn>
>> Dear all,
>> Recently, I want to add angle_restraints and dihedral_restraints for
>> 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
>> 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
>> 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
>> 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
>> 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
> directives require this.
> pdb2gmx -h will help here.
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