[gmx-users] sigma and epsilon.
Peter C. Lai
pcl at uab.edu
Mon Apr 30 18:14:03 CEST 2012
you will have to find the parameters for a carbocation in this configuration from someone who has derived them before, if acpype doesn't know about the species in this configuration, or derive them yourself using ab initio/semiempiracle methods (i.e. gaussian). Also remember you'll need angle and dihedral parameters too (so the pairwise vdw coefficients is not your only problem).
Sent from my Android phone with K-9 Mail. Please excuse my brevity.
chip <chip at bio.gnu.ac.kr> wrote:
Please anybody help me
I'm trying to simulate a protein-ligand complex system using GROMACS 4.5.3 and Amber03 forcefield.
In this system, a carbocationic intermediate was used as ligand
C - C+ - C - C - O-PP (Carbocationic intermediate)
I tried to obtain topology file for intermediate molecule using ACPYPE
[Command: acpype -i intermediate.mol2 -n -2]
But, ACPYPE didn't recognize the carbocation
So, I firstly obtained topology file for substrate molecule
C = C - C - C - O-PP (Substrate: IPP)
[Command: acpype -i IPP.mol2 -n -3]
Then, I tried to modify [atomtypes] in IPP.itp file by adding atomtype for carbocationic carbon
But, I couldn't do this
[ atomtypes ] <--- IPP.itp =================================================================
;name bond_type mass charge ptype sigma epsilon Amb
c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 ; single bonded carbon
c2 c2 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ; double bonded carbon
os os 0.00000 0.00000 A 3.00001e-01 7.11280e-01 ; 1.68 0.1700
p5 p5 0.00000 0.00000 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000
o o 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100
h1 h1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157
hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157
ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150
how to obtain sigma and epsilon values for carbocationinc carbon ?
I've read the manual, but I'm still none the wiser
I'am a lack of knowledge about this
Please kindly give some suggestions and comments
Is it right this way to make the topology file for carbocationic intermediate ?
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users