Hi All,
Yes, probably the problem is with inpcrd file as the output save the
following.
I have tried altering the number of water molecules to reduce the size of
the system but it didn't help, something is wrong with the inpcrd.
Is it the box information in inpcrd that's wrong?
Can you please suggest how to fix this?
Thanks a lot.
Vaibhav
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
|
Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
peek_ewald_inpcrd: SHOULD NOT BE HERE
On Tue, Apr 21, 2015 at 1:57 PM, Kenneth Huang <kennethneltharion.gmail.com>
wrote:
> Vaibhav,
>
> It seems to suggest that there's something wrong with the inpcrd, or at
> least with how you made it. A lot of the earlier messages on the mailing
> list seem to indicate how the issue is sourced back to things not present
> in the inpcrd, specifically the periodic box dimensions (
> http://archive.ambermd.org/201206/0058.html).
>
> Another possibility- how large is your system? I think I've run into the
> same message before with trying to minimize extremely large systems
> without enough memory available on the machine, so you could try testing it
> on a machine with more available memory, or trying to cut the atom count in
> your system.
>
> Best,
>
> Kenneth
>
> On Tue, Apr 21, 2015 at 5:29 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
> >
>
>
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
> _______________________________________________
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> 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
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Received on Tue Apr 21 2015 - 06:30:03 PDT
