Thank you very much for reply. The folowings are my input and part of output
files of the short minimization(I did not use ntmin=2). The VDWAALS continued
decreasing until the running clashed at NSTEP=448, EEL seemed to keep stable but
the 1-4 EEL was abnormal. Do I need to run just steepest descent (ntmin=2) for
any minimization course before MD or just when I check the problems? I ran it
with ntmin=2 for 1000 steps just now, nothing strange happened.
The initial structure of the molecule looks good in xleap. All the atoms are in
the proper shapes of the molecule except some close distances. How can I fix the
initial coordinate if possible? Thanks a lot.
minimization with sander (Amber7)
&cntrl
imin = 1, maxcyc = 500, drms = 0.0005, ntb = 0,
ntpr = 1, cut = 999., ncyc = 100,
&end
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.6975E+07 6.2734E+07 4.6004E+08 OS2 3
BOND = 0.0444 ANGLE = 19.7530 DIHED = 40.0723
VDWAALS = 26975175.0840 EEL = -356.7031 HBOND = 0.0000
1-4 VDW = 23.2733 1-4 EEL = 134.5024 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2 2.3317E+07 5.3553E+07 3.9271E+08 OS2 3
BOND = 0.0496 ANGLE = 19.7561 DIHED = 40.0699
VDWAALS = 23317575.3967 EEL = -355.6838 HBOND = 0.0000
1-4 VDW = 23.2749 1-4 EEL = 134.4709 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
3 1.9624E+07 4.4402E+07 3.2561E+08 OS2 3
BOND = 0.0689 ANGLE = 19.7628 DIHED = 40.0671
VDWAALS = 19623718.0502 EEL = -354.4973 HBOND = 0.0000
1-4 VDW = 23.2769 1-4 EEL = 134.4331 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
4 1.6008E+07 3.5585E+07 2.6096E+08 OS2 3
BOND = 0.1110 ANGLE = 19.7754 DIHED = 40.0638
VDWAALS = 16008633.7331 EEL = -353.1240 HBOND = 0.0000
1-4 VDW = 23.2794 1-4 EEL = 134.3876 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
5 1.2597E+07 2.7418E+07 2.0106E+08 OS2 3
BOND = 0.1884 ANGLE = 19.7969 DIHED = 40.0598
VDWAALS = 12597448.0391 EEL = -351.5451 HBOND = 0.0000
1-4 VDW = 23.2826 1-4 EEL = 134.3329 RESTRAINT = 0.0000
.....................................
NSTEP ENERGY RMS GMAX NAME NUMBER
20 5.0931E+03 1.9272E+03 1.2111E+04 OS1 1
BOND = 90.4811 ANGLE = 46.1183 DIHED = 40.4325
VDWAALS = 5073.8928 EEL = -309.6778 HBOND = 0.0000
1-4 VDW = 23.4222 1-4 EEL = 128.4132 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
21 2.5230E+03 8.0402E+02 5.0225E+03 OS1 1
BOND = 129.7152 ANGLE = 57.0599 DIHED = 40.7277
VDWAALS = 2453.6579 EEL = -308.5802 HBOND = 0.0000
1-4 VDW = 23.6126 1-4 EEL = 126.8305 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
22 1.2918E+03 3.0742E+02 1.8284E+03 OS1 1
BOND = 180.0818 ANGLE = 70.9464 DIHED = 41.1118
VDWAALS = 1159.6853 EEL = -308.4666 HBOND = 0.0000
1-4 VDW = 23.8184 1-4 EEL = 124.6317 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
23 7.3901E+02 1.2391E+02 5.8976E+02 OS1 1
BOND = 223.1975 ANGLE = 86.5386 DIHED = 41.5232
VDWAALS = 551.6798 EEL = -309.2346 HBOND = 0.0000
1-4 VDW = 23.8793 1-4 EEL = 121.4282 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
24 4.3500E+02 6.6137E+01 2.3628E+02 C4 30
BOND = 191.0547 ANGLE = 99.9813 DIHED = 41.7831
VDWAALS = 271.9957 EEL = -310.3165 HBOND = 0.0000
1-4 VDW = 23.4163 1-4 EEL = 117.0840 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
25 2.3600E+02 3.5446E+01 1.5606E+02 OS3 4
BOND = 90.7128 ANGLE = 115.9359 DIHED = 42.2194
VDWAALS = 162.9209 EEL = -310.4972 HBOND = 0.0000
1-4 VDW = 22.5567 1-4 EEL = 112.1513 RESTRAINT = 0.0000
.............................................
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -6.8263E+01 6.0943E+00 2.7356E+01 H51 16
BOND = 11.8026 ANGLE = 73.8867 DIHED = 42.8092
VDWAALS = 11.9175 EEL = -301.8189 HBOND = 0.0000
1-4 VDW = 12.3018 1-4 EEL = 80.8380 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
51 -6.8544E+01 9.8322E+00 5.2987E+01 O50 15
BOND = 11.4579 ANGLE = 75.9026 DIHED = 42.9217
VDWAALS = 10.0194 EEL = -301.6093 HBOND = 0.0000
1-4 VDW = 12.2386 1-4 EEL = 80.5254 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
52 -6.8780E+01 1.2245E+01 7.7299E+01 C33 36
BOND = 14.5858 ANGLE = 72.2719 DIHED = 42.8744
VDWAALS = 11.0461 EEL = -301.7738 HBOND = 0.0000
1-4 VDW = 11.9915 1-4 EEL = 80.2241 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
53 -6.6980E+01 1.7013E+01 1.2063E+02 C33 36
BOND = 13.6907 ANGLE = 76.1965 DIHED = 43.0121
VDWAALS = 9.2574 EEL = -301.5052 HBOND = 0.0000
1-4 VDW = 12.2896 1-4 EEL = 80.0787 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
54 -7.4094E+01 3.9067E+00 1.7504E+01 O50 15
BOND = 9.8693 ANGLE = 73.2662 DIHED = 42.9774
VDWAALS = 9.4424 EEL = -301.5919 HBOND = 0.0000
1-4 VDW = 12.0006 1-4 EEL = 79.9416 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
55 -7.5453E+01 6.7734E+00 3.3126E+01 O50 15
BOND = 11.1981 ANGLE = 71.0947 DIHED = 43.0075
VDWAALS = 9.4969 EEL = -301.6273 HBOND = 0.0000
1-4 VDW = 11.8687 1-4 EEL = 79.5084 RESTRAINT = 0.0000
...............................................
NSTEP ENERGY RMS GMAX NAME NUMBER
326 -1.4564E+02 1.8635E+00 8.3872E+00 C31 42
BOND = 4.5021 ANGLE = 48.7269 DIHED = 44.7938
VDWAALS = -11.6501 EEL = -311.9779 HBOND = 0.0000
1-4 VDW = 12.4539 1-4 EEL = 67.5101 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
327 -1.4570E+02 1.6158E+00 7.2094E+00 C31 42
BOND = 4.4931 ANGLE = 48.6876 DIHED = 44.7936
VDWAALS = -11.6516 EEL = -311.9912 HBOND = 0.0000
1-4 VDW = 12.4552 1-4 EEL = 67.5126 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
328 -1.4576E+02 1.3853E+00 5.9196E+00 C31 42
BOND = 4.4956 ANGLE = 48.6350 DIHED = 44.7949
VDWAALS = -11.6537 EEL = -312.0115 HBOND = 0.0000
1-4 VDW = 12.4562 1-4 EEL = 67.5212 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
329 -1.4583E+02 1.1848E+00 4.6123E+00 C31 42
BOND = 4.5116 ANGLE = 48.5651 DIHED = 44.7987
VDWAALS = -11.6564 EEL = -312.0418 HBOND = 0.0000
1-4 VDW = 12.4566 1-4 EEL = 67.5408 RESTRAINT = 0.0000
.......................................................
NSTEP ENERGY RMS GMAX NAME NUMBER
445 5.9643E-01 4.9484E+01 3.4419E+02 O41 48
BOND = 118.4773 ANGLE = 120.6025 DIHED = 53.2918
VDWAALS = -12.3050 EEL = -305.5181 HBOND = 0.0000
1-4 VDW = 12.2175 1-4 EEL = 13.8304 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
446 -2.5247E+03 7.9332E+03 5.2102E+04 O41 48
BOND = 119.2712 ANGLE = 146.2262 DIHED = 52.5048
VDWAALS = -12.2562 EEL = -302.8007 HBOND = 0.0000
1-4 VDW = 12.4022 1-4 EEL = -2540.0104 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
447 -3.0601E+05 1.0647E+08 8.2860E+08 H54 51
BOND = 120.7894 ANGLE = 148.1497 DIHED = 52.4627
VDWAALS = -12.2550 EEL = -302.7370 HBOND = 0.0000
1-4 VDW = 12.4228 1-4 EEL = -306025.0251 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
448 -3.1064E+05 1.0972E+08 8.2030E+08 H54 51
BOND = 120.7918 ANGLE = 148.1526 DIHED = 52.4626
VDWAALS = -12.2549 EEL = -302.7369 HBOND = 0.0000
1-4 VDW = 12.4228 1-4 EEL = -310660.0186 RESTRAINT = 0.0000
Frac coord min, max: -116.333726 117.209705
The system has extended beyond
the extent of the virtual box.
Quoting "David A. Case" <case.scripps.edu>:
> On Tue, Feb 17, 2004, L Jin wrote:
> >
> > After I load amber prep file into xleap, I used check unit and was given
> the
> > following message:
> >
> > Unit Editor: Warning: Close contact of 0.323280 angstroms between .R<4SN
> > 1>.A<ON3 25> and .R<4SN 1>.A<H51 29>
>
> ...etc
>
> >
> > I know they are just some warnings and I can save my prmtop and inpcrd
> files
> > without problems. But I suspect the Close Contact warnings are the reason
> > which make the subsequent minimizaion clash with the following abnormal
> > errors:
> >
> > Frac coord min, max: -116.333726 117.209705
> > The system has extended beyond
> > the extent of the virtual box.
>
> It is certainly true that such very bad contacts could cause minimizations
> to fail in this way, but it is unusual. How many steps have you run before
> you get the above failure?
>
> >
> > I have run some short minimizaiton and got the output files every step.
> And
> > I found that the problems seem to be the VDWAALS = 26975175.0840 EEL
> =
> > -356.7031.
>
> This initial vdW energy should not cause the kinds of problems you state.
> What happnes to these energies during the course of the "short
> minimizations"?
> Run just steepest descent (ntmin=2) if you have not been doing that. I
> would
> think that after 50 steps of minimization, you should have acceptable
> energies. But you may have such a bad initial structure (what does it look
> like visually) that Amber is unable to correct it. In that case, you will
> have to fix the starting coords.
>
> ..good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case.scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
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Received on Tue Feb 17 2004 - 18:53:00 PST
