The description for the Urey-Bradley potential (assuming two quadratic
terms qualify for the proud term "potential") is described in the user
manual, and the constants' order of appearance in the itp file is given
in the Table 5.5 of the manual. If you have a basic quadratic angular
term (first term in U-B with two constants) from elsewhere and you want
to use it in the U-B format, it is an absolutely trivial task. All you
have to do is set the U-B distance-dependent energy component to zero.
Alex
On 12/20/2017 12:05 AM, RAHUL SURESH wrote:
Hi
Thank you Mark.
On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
Sorry I don't know how any of these non-GROMACS tools work, or even whether
they actually generate Urey Bradley interactions that have all the terms. I
suggest you spend some time with the documentation.
Mark
On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH <drrahulsur...@gmail.com>
wrote:
Sorry Mark, I failed to note that.
I am afraid that I don't know what that are those components and how and
where to find it. If you are actually meaning about "ub0 kub"
components,
how could i find the value for it. In case of swiss param generated itp
file, these components appear to be 0. Any help here please?
On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham <mark.j.abra...@gmail.com
wrote:
Hi,
Please read my answer.
Mark
On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH <drrahulsur...@gmail.com>
wrote:
On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 12/19/17 11:14 AM, RAHUL SURESH wrote:
Dear all
For grompp em.mdp I get an error
ERROR 1 [file THC.itp, line 89]:
Incorrect number of parameters - found 2, expected 4 or 8 for
U-B.
My itp file as follows
[ angles ]
1 2 29 5 79.178 109.588 *{Line 89}*
1 2 3 5 32.192 112.817
2 3 31 5 51.424 109.189
From the manual chapter 5, function of U-B is 5. And it works
fine
for
function type 2 and 8.
Any thing better could be done?
As the error tells you, the U-B functional form requires at least 4
parameters; look at its functional form. See Table 5.5.
Dear Justin
But the parameter obtained from ffTK have only two. What could be
done.?
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
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340 West Campus Dr.
Blacksburg, VA 24061
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