[gmx-users] how to apply distance restrains between a residue and an ion
victordsmagift at gmail.com
Tue Sep 1 22:48:02 CEST 2015
I know it might be a silly question. But can someone please help me out
Thank you so so much!
On Tue, Sep 1, 2015 at 11:54 AM, Victor Ma <victordsmagift at gmail.com> wrote:
> hello all
> I need to apply a distance restraint between a sodium and a residue. I
> read the manual, etc, which seems to suggest adding something like below to
> the .itp file.
> [ distance_restraints ]
> ; ai aj type index type’ low up1 up2 fac
> 10 16 1 0 1 0.0 0.3 0.4 1.0
> 10 28 1 1 1 0.0 0.3 0.4 1.0
> But my protein and ions are in two separate itp file. So how do I do it?
> Also I have multiple sodiums, but in the SOD.itp file, there is only one line
> [ moleculetype ]
> ; name nrexcl
> SOD 1
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 SOD 1 SOD SOD 1 1.000 22.9898 ; qtot 1.000
> So how do I get the atom number for the specific sodium I want to restraint?
> Thank you so much.
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