[gmx-users] Re: Two questions when simulate the protein in lipidbilayer: 1. ratio of water/lipid; 2. ligand charge

[PeiQuan Chen]

Dear Daan van Aalten:
  
  Thank you for kind help.
  But I have something confused with the topol files generated by PRODRG.
The dihedrals parameters I get from the PRODRG is following:
 [ dihedrals ]
 ;ai  aj  ak  al  fu    c0    c1 m  c0   c1 m
   1   2   3   4   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAA  CAB  CAD  CAF
   2   3   4   5   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAB  CAD  CAF  CAE
   3   4   5   6   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAD  CAF  CAE  CAC
   4   5   6   1   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAF  CAE  CAC  CAA
   5   6   1   2   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAE  CAC  CAA  CAB
   6   1   2   3   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAC  CAA  CAB  CAD

But From the ffgmxbon.itp, I have found that:
[ dihedraltypes ]
  ; i    l func        q0          cq
 CR61 CR61    2     0.000     167.360
   
   So the topol files generated by PRODRG is not consistent with the ffgmxbon.itp. Is it a bugs? 


Sincerely yours
---- 
PeiQuan Chen
________________________________________________________________________
PeiQuan Chen 	Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone:	(86)2223506728		Mobile Phone: (+86)13920675030
gromacs at 163.com	
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