AMBER Archive (2008)

Subject: Re: AMBER: LEap error message for parmBSC0 force field

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu Apr 03 2008 - 13:08:58 CDT

Hi Bill,

Thank you for your response.

Here is the parmBSC0 parameters I downloaded via a weblink posted in AMBER website. What additional parameters do you think should be added here?

best regards,

jenk.

torsion chi y gamma
MASS
CI 12.001

BOND
CI-H1 340.0 1.090
CI-CT 310.0 1.526
OS-CI 320.0 1.410
OH-CI 320.0 1.410

ANGLE
H1-CI-CT 50.0 109.50
H1-CI-H1 35.0 109.50
CI-CT-H1 50.0 109.50
CI-CT-OS 50.0 109.50
CI-CT-CT 40.0 109.50
OS-CI-H1 50.0 109.50
OS-CI-CT 50.0 109.50
P -OS-CI 100.0 120.50
OH-CI-H1 50.0 109.50
OH-CI-CT 50.0 109.50
HO-OH-CI 55.0 108.50

DIHE
X -CI-OS-X 3 1.150 0.0 3.0
X -CI-OH-X 3 0.500 0.0 3.0
X -CI-CT-X 9 1.400 0.0 3.0
CT-OS-CT-CI 1 0.383 0.0 -3.0
CT-OS-CT-CI 1 0.100 180.0 2.0
H1-CI-CT-OS 1 0.250 0.0 1.0
H1-CI-CT-OH 1 0.250 0.0 1.0
H1-CT-CI-OS 1 0.250 0.0 1.0
H1-CT-CI-OH 1 0.250 0.0 1.0
CI-CT-CT-CT 1 0.180 0.0 -3.0
CI-CT-CT-CT 1 0.250 180.0 -2.0
CI-CT-CT-CT 1 0.200 180.0 1.0
OS-P -OS-CI 1 0.185181 31.79508 -1.0 alfa
OS-P -OS-CI 1 1.256531 351.95960 -2.0 alfa
OS-P -OS-CI 1 0.354858 357.24748 3.0 alfa
OH-P -OS-CI 1 0.185181 31.79508 -1.0 alfa
OH-P -OS-CI 1 1.256531 351.95960 -2.0 alfa
OH-P -OS-CI 1 0.354858 357.24748 3.0 alfa
CT-CT-CI-OS 1 1.178040 190.97653 -1.0 gamma
CT-CT-CI-OS 1 0.092102 295.63279 -2.0 gamma
CT-CT-CI-OS 1 0.962830 348.09535 3.0 gamma
CT-CT-CI-OH 1 1.178040 190.97653 -1.0 gamma
CT-CT-CI-OH 1 0.092102 295.63279 -2.0 gamma
CT-CT-CI-OH 1 0.962830 348.09535 3.0 gamma

NONB
CI 1.9080 0.1094
 

Bill Ross <ross_at_cgl.ucsf.edu> wrote: ** Warning: No sp2 improper torsion term for OS-H1-CI-CT
        atoms are: O5' H5'2 C5' C4'
 ** Warning: No sp2 improper torsion term for H1-H1-CI-CT
        atoms are: H5'1 H5'2 C5' C4'

If I remember correctly, these messages appear whenever an atom has
3 neighbors and no improper term applies. It is suspicious that this
is happening to C5' (the 3rd atom is the central one) - shouldn't it
have 4 neighbors? (O5', H5'1, H5'2, C4') I.e. possibly in one or more
places you are missing H5'1 and in other(s) a bond to O5'.

Bill
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