trevor brown wrote:
Dear Justin,
Regarding our previous discussion under "CNT" topic, you want to know
exactly what I did to define C-C interaction. I have summarized it below.
1. I copied oplsaa.ff folder in my working directory
2. I added following lines to atomname2type.n2t
C opls_995 0 12.011 2 C 0.142 C 0.142
C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142
C opls_997 0 12.011 4 C 0.142 C 0.142 C 0.142 C 0.142
C opls_998 0 12.011 5 C 0.142 C 0.142 C 0.142 C 0.142
C 0.142
3. I added those to atomtypes.atp
opls_995 12.01100 ;
opls_996 12.01100 ;
opls_997 12.01100 ;
opls_998 12.01100 ;
4. I added those to ffbonded.itp
[ bondtypes ]
C C 1 0.14210 478900
[ angletypes ]
C C C 1 120.000 562.2
[ dihedraltypes ]
5. I constructed .top file for CNT with the following, then I converted
it into .itp by vi editor
g_x2top -f cnt.gro -o cnt.top -nopairs -nexcl 5
6. By pdb2gmx, I obtained .top for peptide then I converted it into .itp
7. I combined CNT and peptide's pdbs in pymol and saved.
8. I wrote a .top file given below,
;
; File 'topol.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Mon Jan 10 02:51:19 2011
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.3
;
; Command line was:
; pdb2gmx -ignh -f vpgvg10.pdb
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "forcefield.itp"
Be careful with this - if you move this topology between directories, it will
call any forcefield.itp file that may be in the working directory. What did you
remove the "oplsaa.ff" prefix?
; Include topology for CNT
#include "cnt.itp"
; Include topology for UW1
#include "uw1.itp"
; Include water topology
#include "spc.itp"
[ system ]
; Name
Protein and CNT in water
[ molecules ]
; Compound #mols
Protein 1
CNT 1
SOL 4019
9. When I make grompp for minimization it givea me the following error
WARNING 1 [file ffbonded.itp, line 2703]:
Overriding Bond parameters.
old: 0.151 292880 0.151 292880
new: C C 1 0.14210 478900
ERROR 1 [file ffbonded.itp, line 2707]:
Not enough parameters
Generated 334153 of the 334153 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 334153 of the 334153 1-4 parameter combinations
-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: toppush.c, line: 1166
Fatal error:
Atomtype opls_996 not found
That is all what I exactly did. Is anything wrong or missing?
You never defined nonbonded parameters for your new atom type. You've declared
that it exists in the .atp file, but then you didn't add that atom type in
ffnonbonded.itp.
-Justin
best wishes
trevor
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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