[gmx-users] Orienting molecule in a correct direction

[Justin Lemkul]

On 10/30/16 12:03 AM, faride badalkhani wrote:
> Dear all,
>
> I want to define z axis as the reaction coordinate in a series of umbrella
> sampling simulations. As a first step, I use the editconf -prince to orient
> the ligand along the x axis and then I change the x and z columns in an

x and z columns of what?  If you have an orientation aligned along x, and you 
want it aligned along z, it's a simple use of editconf -rotate 0 90 0

> editor. But, every time I get error at pulling step. Could you tell me what
> is wrong?

No, because you haven't told us what the exact error is and all the steps you 
took in between.  There's a lot of work that goes on between setting up an 
orientation and actually running a simulation.

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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