Dear Amber experts,
I have on my Linux server Amber16 and AmberTools16.
I used distance restraints option for several bonds in my protein.
Running minimization script I have received an error message:
Warning: Error opening "Old" file from subroutine OPNMRG
File = rst.dist
I need your help how to resolve the problem.
Please find below all details in the copy of input, output and
rst.dist files.
Thank you,
Michael
-------------------------------------------------------
Amber 16 PMEMD 2016
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 16
| Run on 12/20/2017 at 22:40:52
| Executable path: pmemd.cuda
| Working directory: /var/spool/scratch/shokhen/1gg6_SEM_dist_restr/1a_
| Hostname: enzyme03
[-O]verwriting output
File Assignments:
| MDIN: min2.in
| MDOUT: min2.out
| INPCRD: ../1_/mc_min1.rst
| PARM: /home/enz/shokhen/localdisk/1gg6_SEM_dist_restr/mc.prmtop
| RESTRT: mc_min2.rst
| REFC: /home/enz/shokhen/localdisk/1gg6_SEM_dist_restr/1_/mc_min1.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
| MDINFO: mdinfo
| MDFRC: mdfrc
Here is the input file:
hect_c2: initial minimisation whole system
&cntrl
imin = 1,
maxcyc = 40000,
ncyc = 5000,
ntb = 1, iwrap = 1, nmropt=1,
ntr = 1,
cut = 10.0
&end
&wt TYPE ='END' /
DISANG=rst.dist
Note: ig = -1. Setting random seed to 402242 based on wallclock time in
microseconds.
|
| CUDA_VISIBLE_DEVICES: not set
| CUDA Capable Devices Detected: 4
| CUDA Device ID in use: 1
| CUDA Device Name: GeForce GTX 1080
| CUDA Device Global Mem Size: 8114 MB
| CUDA Device Num Multiprocessors: 20
| CUDA Device Core Freq: 1.73 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 32.823
| New format PARM file being parsed.
| Version = 1.000 Date = 12/17/17 Time = 11:11:27
| 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
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting box info from netcdf restart file
NATOM = 35194 NTYPES = 18 NBONH = 33373 MBONA = 1858
NTHETH = 4053 MTHETA = 2539 NPHIH = 8321 MPHIA = 8156
NHPARM = 0 NPARM = 0 NNB = 62036 NRES = 10778
NBONA = 1858 NTHETA = 2539 NPHIA = 8156 NUMBND = 83
NUMANG = 190 NPTRA = 205 NATYP = 45 NPHB = 1
IFBOX = 2 NMXRS = 30 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Warning: Error opening "Old" file from subroutine OPNMRG
File = rst.dist
rst.dist
#
# 195 SEM OG 246 APF C2 3.0
&rst
ixpk= 0, nxpk= 0, iat= 2850, 3587, r1= 2.50, r2= 2.80, r3= 3.0, r4= 3.3,
rk2=50.0, rk3=50.0, ir6=0, ialtd=0,
&end
#
# 195 SEM OG 246 APF N3 3.0
&rst
ixpk= 0, nxpk= 0, iat= 2850, 3583, r1= 2.50, r2= 2.65, r3= 2.90, r4= 3.20,
rk2=50.0, rk3=50.0, ir6=0, ialtd=0,
&end
#
# 195 SEM N 246 APF O2 3.0
&rst
ixpk= 0, nxpk= 0, iat= 2843, 3592, r1= 2.50, r2= 2.80, r3= 3.00, r4= 3.30,
rk2=50.0, rk3=50.0, ir6=0, ialtd=0,
&end
#
# 193 GLY N 246 APF O2 3.0
&rst
ixpk= 0, nxpk= 0, iat= 2824, 3592, r1= 2.50, r2= 2.80, r3= 3.00, r4= 3.30,
rk2=50.0, rk3=50.0, ir6=0, ialtd=0,
&end
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Received on Wed Dec 20 2017 - 14:00:02 PST
