From: patrick wintrode (pat_wde2_at_yahoo.com)
Date: Mon Oct 09 2006 - 11:00:44 CDT
I'm getting ready to simulate a protein in 4M urea. Looking around on the CHARMm message board, I found the topology/parameters used by Caflisch & Karplus in 1995 (pasted below).
Since that was over a decade ago, does anyone know of a more recent version? Looking around I haven't found any. For those who are more knowledgable about the parameter sets than I am, does the file pasted below look OK, or would I be better off just trying to parametrize it from scratch?
One last question. Can I just paste this into the top.rtf, top.inp and par.inp files and be good to go?
Thanks.
===========================================================
* APPENDIX to RTF definition.
*
20 1 ! Version number
! This file contains the topologies of pc
! by Amedeo Caflisch November 24, 1995
! charges and atomtypes in analogy from top_all22_lipid.inp
!DECL -CA
!DECL -C
!DECL -O
!DECL +N
!DECL +HN
!DECL +CA
!DECl +C1
AUTOGENERATE ANGLES DIHE
DEFA FIRS NONE LAST NONE
RESI UREA 0. ! urea by A. Caflisch December 19, 1995
GROUP
ATOM O O -0.51
ATOM C C 0.51
GROUP
ATOM N1 NH2 -0.62
ATOM H11 H 0.31
ATOM H12 H 0.31
GROUP
ATOM N2 NH2 -0.62
ATOM H21 H 0.31
ATOM H22 H 0.31
BOND O C C N1 C N2 N1 H11 N1 H12
BOND N2 H21 N2 H22
IMPH C O N1 N2
IMPH N1 C H11 H12
IMPH N2 C H21 H22
============================
BONDS
C NH2 471.0 1.33 ! Caflisch for urea, December 19, 1995
ANGLES
NH2 C NH2 60.0 120.0 ! Caflisch for urea, December 19, 1995
NH2 C O 65.0 120.0 ! Caflisch for urea, December 19, 1995
C NH2 H 30.0 120.0 ! Caflisch for urea, December 19, 1995
DIHEDRALS
H NH2 C NH2 1.4000 2 180.00 ! Caflisch for urea, December 19, 1995
O C NH2 H 1.4000 2 180.00 ! Caflisch for urea, December 19, 1995
IMPROPER
C O NH2 NH2 60.0 0 0.0! Caflisch for urea, December 19, 1995
NH2 C H H 20.0000 0 0.0! Caflisch for urea, December 19, 1995
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