Dear Amber community,
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 min.out file, only gives this information.
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 39.667
| New format PARM file being parsed.
| Version = 1.000 Date = 06/11/16 Time = 12:19:12
NATOM = 30204 NTYPES = 3 NBONH = 12585 MBONA = 17619
NTHETH = 25170 MTHETA = 20136 NPHIH = 40272 MPHIA = 20136
NHPARM = 0 NPARM = 0 NNB = 133401 NRES = 2517
NBONA = 17619 NTHETA = 20136 NPHIA = 20136 NUMBND = 3
NUMANG = 3 NPTRA = 1 NATYP = 3 NPHB = 0
IFBOX = 1 NMXRS = 12 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 2532281
| Hollerith 93131
| Integer 3906262
| Max Pairs 2265300
| nblistReal 362448
| nblist Int 1318017
| Total 52235 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
------------------------------------------------
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
/
I had compared the minimisation scrip with some examples on the web, and it seems to be fine.
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?
In case I need to create a new one, How is it done?
I did try to do it using leap with the following commands, but it did not work
source leaprc.ff12SB
loadamberparams br.frcmod
bred = loadpbd try1.pbd
saveamberparm bred box.prmtop box.inpcrd
quit
I would appreciate any comment about this issue. Thanks in advance
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Received on Fri Aug 05 2016 - 07:00:02 PDT
