[gmx-users] position restraint

[Justin Lemkul]

On 8/22/13 7:13 AM, Shima Arasteh wrote:
>
>
> yes, but there was only a typing mistake in my earlier email.

Always copy and paste; don't re-type.

> The error I get still exists when I use the correct itp file:
>
> First made an .itp file of the ion: ion_posre.itp
>
> Then added these line to top file:
> #include "./charmm36-modified.ff/ions.itp"
> #ifdef POSRES_ION
> #include "ion_posre.itp"
> #endif
>
> And added the line to mdp file
>
> define         = -DPOSRES_ION
>

Position restraints must be placed within the [moleculetype] to which they 
correspond.  Right now, you're declaring a force field and then saying you want 
to restrain an ion that does not exist because it hasn't been introduced in the 
topology.

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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