Hi Charles,
Thanks!
I'm using a somewhat older force field (see below. The Lennard-Jones potential
is implemented differently. For example S (radius = 1.05 angstroms) sigma is
3.7458 in this setup. After double checking the formula given (sigma*2^(-5/6))I
believe is wrong - it should include division by 2 . So for S I get
3.7458(0.561)/2 = 1.05 angstroms.
I pretty sure the sigma I should use is 4.635 to approximate r = 1.20 angstroms.
Keith
! the non-bonded parameters are approximately the same as
! DISMAN's large radii for repel=0.9, and as DISMAN's small
! radii for repel=0.75. (ECEPP2)
! the epsilon values are generally not used (and should not be)
! with this force field
! the radius is sigma*2^(-5/6)
!
! eps sigma eps(1:4) sigma(1:4) repel: 1.0
0.9 0.8 0.75
!
radii
nonbonded C 0.0903 3.3409 0.0903 3.3409 ! 1.875
1.688 1.5 1.406
NONBonded C6R 0.05000 3.6349 0.10000 3.1360 ! added 02/19/10 kc
from quanta params
NONBonded CA 0.120 3.3409 0.120 3.3409
NONBonded CB 0.145 3.3409 0.145 3.3409
NONBonded CC 0.145 3.3409 0.145 3.3409
NONBonded CN 0.145 3.3409 0.145 3.3409
NONBonded CP 0.1450 3.3409 0.1450 3.3409
NONBonded CR 0.1200 3.3409 0.1200 3.3409
nonbonded CT 0.0903 3.3409 0.0903 3.3409
NONBonded CV 0.1200 3.3409 0.1200 3.3409
NONBonded CW 0.1200 3.3409 0.1200 3.3409
NONBonded CX 0.1450 3.3409 0.1450 3.3409
nonbonded H 0.0498 2.2272 0.0498 2.2272 ! 1.250
1.125 1.0 0.9375
nonbonded HRNE 0.0498 2.2272 0.0498 2.2272 ! 1.250
1.125 1.0 0.9375
nonbonded HA 0.0045 2.2272 0.0045 2.2272
nonbonded HC 0.0498 2.2272 0.0498 2.2272
nonbonded N 0.1592 3.0068 0.1592 3.0068 ! 1.688
1.519 1.350 1.266
NONBonded NA 0.1592 3.0068 0.1592 3.0068
NONBonded NB 0.1592 3.0068 0.1592 3.0068
nonbonded NC2 0.1592 3.0068 0.1592 3.0068
nonbonded NH1 0.1592 3.0068 0.1592 3.0068
nonbonded NH2 0.1592 3.0068 0.1592 3.0068
nonbonded NH3 0.1592 3.0068 0.1592 3.0068
nonbonded O 0.2342 2.7755 0.2342 2.7755 ! 1.558
1.402 1.246 1.168
nonbonded OC 1.0244 2.7755 1.0244 2.7755
nonbonded OH 0.2342 2.7755 0.2342 2.7755
nonbonded S 0.0239 3.7458 0.0239 3.7458 ! 2.102
1.892 1.682 1.577
Keith L. Constantine, Ph. D.
Sr. Research Investigator II
Mechanistic Biochemistry
Bristol Myers Squibb Research and Development
P.O. Box 4000
Princeton, NJ 08543-4000
Tel: (609)-252-6926
Fax: (609)-252-6012
e-mail: [email protected]
>-----Original Message-----
>From: Charles Schwieters [mailto:[email protected]]
>Sent: Friday, October 18, 2013 2:04 PM
>To: Constantine, Keith
>Cc: Charles Schwieters; [email protected]; Mueller, Luciano;
>Metzler, William
>Subject: Re: changing van der Waals radius without modifying an atom
>type
>
>
>Hi Keith--
>
>> I used:
>>
>> parameter
>> nonbond (resid X and name HN) 0.0498 4.0000 0.0498 4.000
>> end
>>
>> If I am correct, setting sigma to 4.000 should correspond to a
>> radius of ~1.30 angstroms, which is close enough for this
>> application.
>>
>
>
>Rvdw = sigma 2^(1/6) / 2
>
>so, to get a radius of 1.3 angstrom, use sigma=2.316 angstrom.
>
>best regards--
>Charles
This message (including any attachments) may contain confidential, proprietary,
privileged and/or private information. The information is intended to be for
the use of the individual or entity designated above. If you are not the
intended recipient of this message, please notify the sender immediately, and
delete the message and any attachments. Any disclosure, reproduction,
distribution or other use of this message or any attachments by an individual
or entity other than the intended recipient is prohibited.
_______________________________________________
Xplor-nih mailing list
[email protected]
http://cake.cit.nih.gov/mailman/listinfo/xplor-nih
