Hi,
You may find the following system preparation protocol useful:
https://aip.scitation.org/doi/abs/10.1063/5.0013849
On Thu, Aug 27, 2020 at 1:16 PM Ramanathan Rajesh <
ramanathanrajesh30986.gmail.com> wrote:
> I have attached the 3 files.
>
> Thanks for looking into this.
>
>
>
> Ramanathan R
>
>
>
> On Thu, Aug 27, 2020 at 10:31 PM Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>
>
> > Can you also send us the mini.out and the heat.out files , as well as
>
> > the command you typed to run this ?
>
> >
>
> > adrian
>
> >
>
> >
>
> > On 8/27/20 1:37 PM, Ramanathan Rajesh wrote:
>
> > > [External Email]
>
> > >
>
> > > I have recently started using amber(V18).I am doing a simulation for
>
> > > G-quadruplex docked with ligand.After doing the esp calculation from
>
> > > gaussian and resp fit in amber the minimization was completed
>
> > successfully
>
> > > but the heating stage was not running and showing the following error
> in
>
> > > the heat.out file :
>
> > >
>
> > >
>
> > >
>
> > >
>
> > >
>
> > >
>
> > >
>
> > >
>
> > >
>
> > >
>
> > >
>
> > > *vlimit exceeded for step 72; vmax = 34.0245vlimit exceeded for
>
> > step
>
> > > 88; vmax = 38.2067vlimit exceeded for step 97; vmax =
>
> > > 24.1833vlimit exceeded for step 99; vmax = 4184.6232
>
> > Coordinate
>
> > > resetting (SHAKE) cannot be accomplished, deviation is too large
>
> > > NITER, NIT, LL, I and J are : 0 0 140 470 469
>
> > Note:
>
> > > This is usually a symptom of some deeper problem with the
> energetics
>
> > of
>
> > > the system.*
>
> > >
>
> > > i am attaching the input file i used for the heating stage.Could you
>
> > please
>
> > > help me out to fix the problem i am facing .
>
> > >
>
> > > thanking you in advance
>
> > > yours sincerely
>
> > > Ramanathan R
>
> > >
>
> > > _______________________________________________
>
> > > AMBER mailing list
>
> > > AMBER.ambermd.org
>
> > >
>
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=61HtT7DQJpQI9TbTVDTTfMpDdCYzrZvZym2rY9SZqCw&s=-KRjT81S0KzfSTaxzkVF_0mzqmEFzG7QWOEeV4qDMn0&e=
>
> >
>
> > --
>
> > Dr. Adrian E. Roitberg
>
> > V.T. and Louise Jackson Professor in Chemistry
>
> > Department of Chemistry
>
> > University of Florida
>
> > roitberg.ufl.edu
>
> > 352-392-6972
>
> >
>
> > _______________________________________________
>
> > AMBER mailing list
>
> > AMBER.ambermd.org
>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> >
>
> _______________________________________________
>
> AMBER mailing list
>
> AMBER.ambermd.org
>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 04 2020 - 11:30:03 PDT
