Dear Sir/ Madam,
We are using Amber 7 on Red Hat Linux system. While we are performing
a NMR-restrained moleculacular dynamics simulation step using sander,
we could not run a script which include a heating step from 100K to
298K. There I find an error message in the output file:
| Flags:
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
Warning: Error opening "Old" file from subroutine OPNMRG
File = ./Md_RST
Could you please kindly let me know what the problem with our simulation is?
I am sending the input and output files used in sander as attachments.
Thanking you,
Yours Sincerely,
Wimal Pathmasiri.
--
Ph.D. Student
Department of Bioorganic Chemistry
Uppsala University
BMC, Box 581
SE-75123 Uppsala
Sweden.
Phone: 0046184714980
Fax: 004618554495
-------------------------------------------------------
Amber 7 SANDER Scripps/UCSF 2002
-------------------------------------------------------
| Sat Aug 5 00:02:40 2006
[-O]verwriting output
File Assignments:
| MDIN: Int_Md_Heat.in
| MDOUT: Int_Md_Heat.out
|INPCRD: SA_60.2.rst
| PARM: RA_cio_wat.prmtop
|RESTRT: Int_Md_Heat.rst
| REFC: SA_60.2.rst
| MDVEL: mdvel
| MDEN: Int_Md_Heat.nrj
| MDCRD: Int_Md_Heat.mdcrd
|MDINFO: Int_Md_Heat.mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
Initial dynamics w/ belly on RNA, 8.0 cut, SHAKE
&cntrl
nmropt = 1, ipnlty = 1,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
ntc = 2, tol = 0.00001,
ntf = 2, ntb = 2, dielc = 1.0,
cut = 8.0,
scnb = 2.0, scee = 1.2,
ibelly = 0, ntr = 0, imin = 0,
nstlim = 20000,
t = 0.0, dt = 0.0015,
temp0 = 300.0, tempi = 100.0,
ig = 71277, heat = 0.0,
ntt = 1,
tautp = 0.2,
vlimit = 15.0,
ntp = 1, pres0 = 1.0, comp = 44.6,
taup = 0.2, npscal = 1,
jfastw = 0,
&end
&ewald
a=34.9927920 b=37.1218096 c=40.8344006
&end
&wt
type='TEMP0', istep1=0, istep2=2000,
value1=100.0, value2=298.0,
&end
&wt
type='TEMP0', istep1=2001, istep2=20000,
value1=298.0, value2=298.0,
&end
&wt
type='REST', istep1=0, istep2=2000, value1=0.0, value2=1.0,
&end
&wt
type='REST', istep1=2001, istep2=30000, value1=1.0, value2=1.0,
&end
&wt type='END', &end
DISANG=./Md_RST
LISTOUT=POUT
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
Warning: Error opening "Old" file from subroutine OPNMRG
File = ./Md_RST
Initial dynamics w/ belly on RNA, 8.0 cut, SHAKE
&cntrl
nmropt = 1, ipnlty = 1,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
ntc = 2, tol = 0.00001,
ntf = 2, ntb = 2, dielc = 1.0,
cut = 8.0,
scnb = 2.0, scee = 1.2,
ibelly = 0, ntr = 0, imin = 0,
nstlim = 20000,
t = 0.0, dt = 0.0015,
temp0 = 300.0, tempi = 100.0,
ig = 71277, heat = 0.0,
ntt = 1,
tautp = 0.2,
vlimit = 15.0,
ntp = 1, pres0 = 1.0, comp = 44.6,
taup = 0.2, npscal = 1,
jfastw = 0,
&end
&ewald
a=34.9927920 b=37.1218096 c=40.8344006
&end
&wt
type='TEMP0', istep1=0, istep2=2000,
value1=100.0, value2=298.0,
&end
&wt
type='TEMP0', istep1=2001, istep2=20000,
value1=298.0, value2=298.0,
&end
&wt
type='REST', istep1=0, istep2=2000, value1=0.0, value2=1.0,
&end
&wt
type='REST', istep1=2001, istep2=30000, value1=1.0, value2=1.0,
&end
&wt type='END', &end
DISANG=./Md_RST
LISTOUT=POUT
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Received on Wed Aug 16 2006 - 06:07:10 PDT
