Hi Vaibhav,
What is the last line in your inpcrd file? Does it say something like
90.0000 90.0000 90.0000 at the end? I bet it doesn't which means it doesn't
write the box dimensions and the angles to the inpcrd. So when sander
checks for them and cannot find them it gives the error message that you
reported.
HTH
Sajeewa
On Tue, Apr 21, 2015 at 10:05 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Ops, I meant the prmtop and inpcrd are ok in vmd, but the rst file was not
> generated.
>
> On Tue, Apr 21, 2015 at 3:04 PM, Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
> > Hi,
> > I have checked with vmd, and it was OK.
> >
> >
> > On Tue, Apr 21, 2015 at 2:54 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> Can you read the restart file with cpptraj or vmd or some other program?
> >>
> >> -Dan
> >>
> >> On Tue, Apr 21, 2015 at 3:29 AM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >
> >> wrote:
> >> > Hi All,
> >> > while trying to run the minimization job on prmtop and inpcrd file
> >> > generated using ff14SB force field I am getting the this error message
> >> in
> >> > the out file and sander quits quickly.
> >> > I have checked the unit before generating prmtop and inpcrd file and
> it
> >> > gave no error.
> >> > I am giving the following input to the sander.
> >> >
> >> > Another thread discussing similar error did not offer a clear solution
> >> in
> >> > my case. http://archive.ambermd.org/201411/0298.html
> >> >
> >> > Any hints to trouble shoot this are much appreciated.
> >> > Thanks a lot.
> >> >
> >> > min.in
> >> > --------
> >> > P450 1W0E apo: initial minimization prior to
> >> > MD
> >> > &cntrl
> >> >
> >> >
> >> > imin=1,maxcyc=1000,ncyc=500,
> >> >
> >> >
> >> > ntpr=5,
> >> >
> >> >
> >> > cut=8.0,
> >> >
> >> >
> >> > ntc=2,
> >> >
> >> > ntr=1, restraintmask =
> >> > '.CA,C,O,N',
> >> >
> >> > restraint_wt=1.0
> >> >
> >> > /
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > With Regards.
> >> >
> >> > Dr. Vaibhav A. Dixit,
> >> > Postdoctoral Research Scientist,
> >> > Etherow F40/6,
> >> > AstraZeneca,
> >> > Charter Way,
> >> > Silk Road Business Park,
> >> > Macclesfield,
> >> > Cheshire,
> >> > England,
> >> > SK10 2NX
> >> > Ext. No. 20278
> >> > Email: Vaibhav.Dixit.astrazeneca.com
> >> > Moblie Number: +44-7448233157, +91-7709129400.
> >> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >> >
> >> > Please consider the environment before printing this e-mail
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > With Regards.
> >
> > Dr. Vaibhav A. Dixit,
> > Postdoctoral Research Scientist,
> > Etherow F40/6,
> > AstraZeneca,
> > Charter Way,
> > Silk Road Business Park,
> > Macclesfield,
> > Cheshire,
> > England,
> > SK10 2NX
> > Ext. No. 20278
> > Email: Vaibhav.Dixit.astrazeneca.com
> > Moblie Number: +44-7448233157, +91-7709129400.
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > Please consider the environment before printing this e-mail
> >
>
>
>
> --
> With Regards.
>
> Dr. Vaibhav A. Dixit,
> Postdoctoral Research Scientist,
> Etherow F40/6,
> AstraZeneca,
> Charter Way,
> Silk Road Business Park,
> Macclesfield,
> Cheshire,
> England,
> SK10 2NX
> Ext. No. 20278
> Email: Vaibhav.Dixit.astrazeneca.com
> Moblie Number: +44-7448233157, +91-7709129400.
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 21 2015 - 08:00:02 PDT
