Dear Amber users,
I have been carrying out a simulation of a protein-ligand explicit water MD
simulation using the ff99SB force-field. After completing about 50ns of the
run, suddenly the output .rst file of my run had "************" signs
instead of the x-co-ordinates of the 3 atoms of a certain water molecule.
Something like this:
362.5312633 267.2621357-103.1379393-153.5429259-199.6611347-123.3177335
-153.8078616-198.8575496-122.8701936-152.7184258-199.9079292-122.8987778
44.5051355-207.9254210 59.0354869 43.9546665-207.7149791 59.7897613
45.4000580-207.7895160 59.3467348************ 74.1218262-104.0510373
************ 73.6745789-103.2063682************ 73.5659402-104.5814460
-365.9189866 447.8853764 -30.3888650-365.5955834 447.5974812 -31.2425385
-365.7685621 447.1372462 -29.8110194-104.6516299 88.9232533 -40.5432262
-104.7796026 89.8573816 -40.7083297-104.1181933 88.6209863 -41.2782853
245.4157167 244.9111976 456.5944703 244.8351246 245.6404763 456.3769909
245.4239023 244.3682718 455.8061833 519.1683584 -99.5645316 -49.2072520
Cause of this, I could not restart my run and hence had to generate yet
another .rst file of an earlier frame from the same run using the ptraj
module. I then renamed the new .rst file as a .crd file and changed the ntx
= 7, irest = 1, to ntx = 1, irest = 0, in the .in file for the new run.
when I submit this particular run my job gets stuck at a particular position
and does not move further.
File Assignments:
| MDIN: pr55.in
| MDOUT: pr55.out
|INPCRD: pr544.crd
| PARM: top_leap.top
|RESTRT: pr55.rst
| REFC: pr544.crd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: pr55.crd
|MDINFO: pr55.info
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
rm to 300K quickly,
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 100, ntwx = 500, ntwe = 0,
ntc = 2, ntf = 2,
nstlim = 1000000, dt =0.002,
tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
ntb = 2, ntp = 1, taup = 0.2, pres0 =1.0,ntr=0
&end
END
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
I do not kno how to move further ahead with it. If any one has ever faced
this problem, it would be great if you could help me out.
Also if any one knows, why the software generated the "************" signs
in my .rst file in the first place, please do let me kno.
thanks in advance..
Mufaddal
--
Soni Mufaddal Saifee
Fourth (Senior) Year B.Tech
Dept. of Biotechnology
IIT Madras.
"The will of God will never take you where the grace of God will not protect
you."
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 08 2009 - 01:07:19 PDT
