Hi,
The large energy means your topology is probably broken. Please use a tool
that will write an .itp file for you (e.g. SwissParam?), or next time get
your topology for your ligand working before you try to use it in a
complex. Even get a simple form of the ligand working first, to teach
yoursel
To be included here, the ligand I have uploaded seems to be so congested
and out of form. Look literally like a clumsy ball.
I am not sure what make this happen.
On Wed, Dec 20, 2017 at 2:51 PM, RAHUL SURESH
wrote:
> Dear Alex
>
> I have tried that but the system collapse. For em_real.mdp option
Dear Alex
I have tried that but the system collapse. For em_real.mdp option,I get
message stating
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a
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
Hi
Thank you Mark.
On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham
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.
>
>
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 wrote:
> Sorry Mark, I failed to note
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
Hi,
Please read my answer.
Mark
On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH wrote:
> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul 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
On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul 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 foll
Hi,
The CHARMM software implements UB with two separate bond and angle
components, which you probably have to find and to insert here, to suit the
way GROMACS implements the interaction in a self-contained way.
Mark
On Wed, Dec 20, 2017, 10:36 AM Justin Lemkul wrote:
>
>
> On 12/19/17 11:14 AM
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 29 579.178 109.588 *{Line 89}*
1 2 3 5
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 29 579.178 109.588 *{Line 89}*
1 2 3 532.192 112.817
2 3 31 551.424 10
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 29 579.178 109.588 *{Line 89}*
1 2 3 532.192 112.817
2 3 31 551.424 10
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