On 1/14/13 9:04 PM, learnmd wrote:
Justin,
Thanks for the direction.
So, I have now edited spc template to create a new model called spchw.
The spchw.itp for amber99 forcefield now looks like this:
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; id at type res nr res name at name cg nr charge mass
1 OW_spch 1 SOL OW 1 -0.870 15.99940
2 HW_spch 1 SOL HW1 1 0.435 2.00800
3 HW_spch 1 SOL HW2 1 0.435 2.00800
#ifndef FLEXIBLE
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330
[ exclusions ]
1 2 3
2 1 3
3 1 2
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.1 345000 0.1 345000
[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.43 383 109.47 383
#endif
I have also edited the ffnonbonded.itp file for amber99 to include this
model
atomtypes ]
; name at.num mass charge ptype sigma epsilon
Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00
; spch water - use only with spch.itp & settles
OW_spch 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01
HW_spch 1 2.0080 0.0000 A 0.00000e+00 0.00000e+00
Please advise if this is sufficient.
In principle. Try it and see.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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