Hello Dear Amber Users!
Thaks for anwsering my questions.
At this moment I have to ask some more questions :-)
I have done minimisation in two ways (explicit and implicit water).
I know the difference but how do I know which model is better?
Should I decide about this looking at my output files?
Is igb=2 better than igb=1 for proteins with bigger solvent space?
Can anyone send me some papers about choosing the right solvent?
Here are some examples of my work trying to minimise my structure:
1) Explicit water without restrains:
Input:
&cntrl
imin=1,
maxcyc=2500,
ncyc=500,
cut=10.0,
ntb=1,
ntr=0,
ntc=2, ntf=2
/
end of output:
NSTEP ENERGY RMS GMAX NAME
NUMBER
2500 -9.5821E+04 1.7828E+01 1.8903E+02
H26 4186
BOND = 160.8325 ANGLE = 751.0722 DIHED
= 2416.1475
VDWAALS = 16711.7024 EEL = -126656.4899 HBOND
= 0.0000
1-4 VDW = 887.6797 1-4 EEL = 9907.5830 RESTRAINT
= 0.0000
( about 1400 steps:
NSTEP ENERGY RMS GMAX NAME
NUMBER
1400 -9.5822E+04 1.7829E+01 1.8923E+02
H26 4186
BOND = 160.8431 ANGLE = 751.0710 DIHED
= 2416.1423
VDWAALS = 16712.1417 EEL = -126656.9667 HBOND
= 0.0000
1-4 VDW = 887.6811 1-4 EEL = 9907.5844 RESTRAINT
= 0.0000
..... RESTARTED DUE TO LINMIN FAILURE ...
) - Failure is not a good sign I think :-)
2) Implicit water (here cut is a bit bigger - trying on my own.. )
Input:
&cntrl
imin=1, maxcyc=1000, ncyc=300,
scee=1.2, cut=17.0, ntb=0,
igb=1,
/
Output:
NSTEP ENERGY RMS GMAX NAME
NUMBER
1000 -1.1216E+04 1.3855E+00 5.9929E+01
CG 1229
BOND = 175.6606 ANGLE = 696.7887 DIHED
= 2259.0592
VDWAALS = -2128.5296 EEL = -18267.1712 EGB
= -4605.8447
1-4 VDW = 843.8061 1-4 EEL = 9810.5691 RESTRAINT
= 0.0000
3) Minimisation in explicit water without restrains:
Input:
&cntrl
imin=1, maxcyc=20000, ncyc=5000,
scee=1.2, cut=17.0, ntb=2, ntp=1,
dielc=1.0,
nsnb=20,
ntpr=5,
&end
Output:
NSTEP ENERGY RMS GMAX NAME
NUMBER
2960 -4.7799E+07 8.0983E+10 2.1738E+13
H 4153
BOND = 16488.2521 ANGLE = 844.0407 DIHED
= 2395.0702
VDWAALS = 41551.6173 EEL = -287740.9301 HBOND
= 0.0000
1-4 VDW = 873.5359 1-4 EEL = ************* RESTRAINT
= 0.0000
-------------------------------------------------------------------
I know my cut off is too big. It should be about 8-10.
My minimisation steps should be much shorter. I think a good value
is about maxcyc=2500 and ncyc=500 (but this is just my opinion).
Please tell me if I have some more bad values in my inputs.
Why in the explicit water the EEL is so big?
PS. Dear Yam - thanks for trying, but turning off shake did onley my
minimisation longer :-)
--
Tylko w sierpniu Avanti także w wersji MINI - z łatwością zmieści się w torebce!
http://www.avantimoda.pl
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Received on Thu Aug 11 2005 - 08:53:00 PDT
