[gmx-users] Dihedral Restrain Syntax 4.6

[Justin Lemkul]

On 8/14/14, 10:02 AM, Johnny Lu wrote:
> I forget to mention that in the alanine dipeptide topol.top that I made, I
> tried:
> [ dihedral_restraints ]
>    12 11 13 15 1 1 90 0 2000.0 1
> #endif
>
> but,
> Program grompp, VERSION 4.6.5
> Source code file: /build/buildd/gromacs-4.6.5/src/kernel/toppush.c, line:
> 1914
>
> Fatal error:
> Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest..
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>

Manual section 4.3.3 and Table 5.5 allude to the proper usage, though admittedly 
I see that Table 5.5 is incorrect, as it is missing the value of k.

Going into the code, the proper syntax is to specify the four atoms to be 
restrained and phi, dphi, k as the 3 parameters that the fatal error suggests. 
I don't know what function type to set, probably just 1.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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