[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 ?







Chanin Park

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