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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Received on Sun Aug 07 2016 - 04:30:02 PDT
