Hello Amber Users,
I have problem in minimizing my system protein+nonstandard residue in it.always The my system stop at the same step. and this is the result from the out file, It seems that the EEL option decrease dramaticly. I check the whole structure using check command in xleap but nothing is unusual with that. my non-standard residue in this system hase a phosphate -O-P-O(OH) {charged -1}group with one oxygen protonated. Also I had a system which the phosphate has the charge -2, and this system minimize well.
what might my problem be
The output of Crash job:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.2460E+05 9.1423E-01 5.4017E+01 MG 7228
BOND = 23360.7273 ANGLE = 1087.4903 DIHED = 2060.9859
VDWAALS = 53067.6290 EEL = -426051.6303 HBOND = 0.0000
1-4 VDW = 2051.4105 1-4 EEL = 19823.5159 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -3.2609E+05 1.5365E+00 3.4073E+02 O 5773
BOND = 23575.1875 ANGLE = 1163.3346 DIHED = 2177.9326
VDWAALS = 53060.1856 EEL = -427085.4020 HBOND = 0.0000
1-4 VDW = 1644.4478 1-4 EEL = 19378.7111 RESTRAINT = 0.0000
.... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -7.3925E+05 7.9207E+06 2.4003E+09 H10 7257
BOND = 23572.4859 ANGLE = 1128.0558 DIHED = 2176.8052
VDWAALS = 53031.1008 EEL = -840174.7802 HBOND = 0.0000
1-4 VDW = 1643.9059 1-4 EEL = 19370.0635 RESTRAINT = 0.0000
I really appreciated from your help
Homa
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Received on Tue May 04 2010 - 22:00:04 PDT
