Hi,
On Thu, Oct 6, 2016 at 12:27 PM, Aseel Bala <balaahme.msu.edu> wrote:
> default
>
> 4530
>
> 9.5220000 7.7680000 25.2830000 9.9890000 7.1480000 26.5680000
It's hard to tell from your message, but I suspect that the formatting
of your restart file is not really correct. It's not enough to simply
write the coordinates with 7 decimal places of precision. You need to
have exactly 6 columns, with exactly 12 characters in a column
(fortran is strict about such things). I would recommend that you use
a program that has been created to write such formats, like cpptraj.
For example, to extract frame 3302 from a trajectory file named
Traj.nc and write a restart:
trajin Traj.nc 3302 3302
trajout frame3302.inpcrd restart
Hope this helps,
-Dan
>
> 11.2810000 7.7970000 26.9740000 11.8220000 7.1260000 28.2400000
>
> 12.5300000 5.9010000 27.8530000 11.9050000 5.5240000 27.2280000
>
> 8.7930000 7.0870000 24.8430000 9.0200000 8.7330000 25.3530000
>
> ..
>
> 35.4780000 35.5360000 35.5240000
>
>
>
> Where the first line is an arbitrary title, the second is the number of
> atoms in the frame and the other lines have the x,y,z coordinates of each
> atom with 6 decimal places. The last line contains size of the periodic box.
> I followed the format for inpcrd here
> (http://ambermd.org/formats.html#restart) to create this file.
>
> The problem is when I run sander from the command line:
> sander -O -i qmmm_in.in -o qmmm.out -c frame3302.inpcrd -p
> simbox.prmtop -r qmmm.rst
>
>
>
> I get the following in the output file:
>
>
>
>
>
> -------------------------------------------------------
>
> Amber 14 SANDER 2014
>
> -------------------------------------------------------
>
>
>
> [-O]verwriting output
>
>
>
> File Assignments:
>
> | MDIN: qmmm_in.in
>
> | MDOUT: qmmm.out
>
> |INPCRD: frame3302.inpcrd
>
> | PARM: simbox.prmtop
>
> |RESTRT: qmmm.rst
>
> | REFC: refc
>
> | MDVEL: mdvel
>
> | MDFRC: mdfrc
>
> | MDEN: mden
>
> | MDCRD: mdcrd
>
> |MDINFO: mdinfo
>
> | MTMD: mtmd
>
> |INPDIP: inpdip
>
> |RSTDIP: rstdip
>
> |INPTRA: inptraj
>
>
>
>
>
> Here is the input file:
>
>
>
> Testing tutorial on website for QMMM with Gaussian
>
> &cntrl
>
> ifqnt=1
>
> &end
>
> &qmmm
>
> qmmask=':31',
>
> qmcharge=0,
>
> qm_theory='EXTERN',
>
> qmcut=15.0
>
> &end
>
> &gau
>
> method = BLYP,
>
> basis = 6-31G,
>
> charge = 0,
>
> &end
>
>
>
> ----------------------------------------------------------------------------
> ----
>
> 1. RESOURCE USE:
>
> ----------------------------------------------------------------------------
> ----
>
>
>
> | Flags:
>
> getting new box info from bottom of inpcrd
>
> | INFO: Old style inpcrd file read
>
>
>
> ERROR: Problem reading coordinates or velocities from frame3302.inpcrd
>
>
>
> I could not understand line 3 :
>
> 9.5220000 7.7680000 25.2830000 9.9890000 7.1480000 26.5680000
>
>
>
>
>
> I'm not seeing what I am doing wrong. Any help with this will be very much
> appreciated. If I have forgotten to mention any important information,
> please let me know.
>
> Thank you very much,
>
>
>
> --
>
>
>
> Aseel Bala
>
> PhD Candidate, Chemical Engineering
>
> Michigan State University
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Oct 06 2016 - 18:00:03 PDT
