[gmx-users] is there extra parameters in .mdp file for running successful angle_restraints?

[jnsong]

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 <jnsong at 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