Does 'trajout out_frame.rst7 ...' not work? What command(s) (if any)
did you try?
-Dan
On Sun, Aug 7, 2016 at 5:01 AM, Stregone <stregone.protonmail.com> wrote:
> Dear Dr. Andreas W. Goetz,
> I am shame for such error!!. As you wrote, that change fixed the error.
> Regarding the further simulations, when I extract the frames. first I did it in pdb in order to
> take at look at the box.
>
> parm box.prmtop
> trajin a.mdcrd
> trajout out_frame.pdb pdb onlyframes 18294,14216,13499,2611 multi
>
> Now, I must extract the inpcrd (rst) input initial coordinates,
> I had assumed that I could use the same commands as above,
> to extract them. However, looks I was wrong.
> is it there a form to extract the coordinates as rst or inpcrd, as
> I did it previously in pdb.
> Thanks in advance
>
>
>
>
>
> -------- Original Message --------
> Subject: Re: [AMBER] QMMM MD, Simulation does not start
> Local Time: August 5, 2016 9:31 PM
> UTC Time: August 5, 2016 9:31 PM
> From: agoetz.sdsc.edu
> To: stregone.protonmail.com,amber.ambermd.org
>
>> I am using Amber 2014 for running a QMMM job.
>> Based on the manual, I prepared the solvent box using LEAP.
>> When I did star the job, I got this error in one of the files:
>>
>> At line 422 of file qm2_read_nm_and_alloc.F90 (unit = 5, file = 'min.in')
>>> Fortran runtime error: End of file
>>> real 0m1.283s
>>> user 0m0.084s
>>> sys 0m0.019s
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>
>> The minimisation script is :
>> minimisation
>> &cntrl
>> imin = 1, maxcyc = 80000, ntmin = 1,
>> ntx = 1,
>> ncyc = 25000,
>> ntb = 1, ntp = 0,
>> cut = 13.0, ifqnt=1
>> /
>> &qmmm
>> qmmask='.1-12',
>> qmcharge=0,
>> qm_theory='PM3',
>> qmshake=0,
>> qm_ewald=1, qm_pme=1
>> /
>
> Try adding a line break or empty line after the end of the &qmmm namelist (after the “/“). This should fix the error.
>
> Your cutoff of 13.0 Angstrom is larger than necessary. Most people use 9.0 Angstrom.
>
>> After the minimisation is done, I will extract the frames with lowest energy. My question is, could I use the same prmtop for further minimisations, or should I create a new one?
>
> You can keep the same prmtop file as long as you don’t add or delete molecules.
>
> All the best,
> Andy
>
> —
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
>
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--
-------------------------
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)
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Received on Sun Aug 07 2016 - 15:00:02 PDT
