Re: [AMBER] QMMM MD, Simulation does not start

From: Stregone <>
Date: Sun, 07 Aug 2016 07:01:57 -0400

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

> 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 = '')
>> 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,

Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771

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