LEaP used to have a bug where it would truncate inpcrd files. This was
fixed by the second update for AmberTools 14 (see
http://ambermd.org/bugfixesat.html). The bug is explained in the
postscript for interested parties.
So make sure you are using AmberTools 14 and that you have applied all of
the updates (and recompiled afterwards!).
HTH,
Jason
The bug is caused because a file handle pointer is not explicitly closed
(via "fclose" in C). The behavior when this happens is undefined -- either
the contents of the file buffer (which is in memory, but not on disk) get
flushed to the file itself, or they simply go away when the program exits
and the memory is reclaimed. Clearly, here, the buffer is *not* getting
flushed and you are left with a partially-truncated version of the inpcrd
file.
The solution is to close the file handle, which flushes the file buffer (as
is done in the second update).
On Tue, Apr 21, 2015 at 10:45 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Hi,
> thanks for pointing this out. Tail command on the inpcrd file says the
> following.
> Can you please suggest on how to fix this?
> Which parameters should I change in the leap.in file to give a sensible
> inpcrd file?
> Thanks.
> Vaibhav
>
> kmcdwlx005 462% tail P450_test.inpcrd
> 12.9410318 24.7763059 28.5292431 6.0666578 11.2373217 31.8421776
> 5.7263398 10.4381030 32.2442456 5.3605584 11.5374928 31.2698610
> 6.7183050 8.3222530 30.2949099 7.5409119 7.8483008 30.1727990
> 6.9621113 9.1013013 30.7947786 4.2421629 15.0141650 28.1041078
> 4.0966209 15.3281953 28.9965360 3.7646832 15.6326551 27.5511977
> 6.1018012 12.0044198 28.1521968 6.0879580 11.1085292 27.8154266
> 6.8190440 12.0114862 28.7860254 7.9544142 12.4381539 30.1975095
> 7.6961920 13.3598609 30.1959426 7.4229183 12.0411973 30.8875559
> 12.8990331 25.5432326 22.9765180 13.0727209 24.9778748 22.2239033
> 13.3919222 26.3433221 22.7944670 8.3746098 8.5713
> ukmcdwlx005 463%
>
> My current leap.in
> ukmcdwlx005 463% more leap.in
> source leaprc.ff14SB
> source leaprc.gaff
> CYP = loadmol2 CYS_HS.mol2
> set CYP head CYP.1.N
> set CYP tail CYP.1.C
> desc CYP
> HEM = loadmol2 HEM_pentacoordinateHS.mol2
> loadamberparams HEM_HS.frcmod
> loadamberparams frcmod.ionsjc_tip3p
> P450 = loadpdb 1W0E_P450_leap.pdb
> bond P450.419.SG P450.477.FE
> solvateoct P450 TIP3PBOX 12
> charge P450
> addions P450 Cl- 0
>
> On Tue, Apr 21, 2015 at 3:39 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com>
> wrote:
>
> > 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
> > >
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 21 2015 - 08:30:04 PDT
