[gmx-users] is there extra parameters in .mdp file for running successful angle_restraints?
mark.j.abraham at gmail.com
Tue May 21 14:43:32 CEST 2013
On Tue, May 21, 2013 at 11:31 AM, jnsong <jnsong at itcs.ecnu.edu.cn> wrote:
> 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
Table 5.5 and manual 7.3 know more than I do about this ;-)
> (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
There's no prohibition. Whether such a combination is reasonable depends,
and is up to you to judge.
> Thank you very much!
> Best wishes!
> 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> wrote:
>> 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 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
>>> 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.
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