AMBER Archive (2004)

Subject: AMBER: Setting up thermodynamic integration

From: david.evans_at_ulsop.ac.uk
Date: Wed Sep 01 2004 - 09:31:10 CDT

Dear list,

My question is about the perturbed bonds, angles etc. when creating a
prmtop file to be used for TI.
I am doing a fairly simple perturbation, where one -CH- group changes
to a -N-

So I use the following commands in my leap.in file:

set complex.90.C2 pertName N1
set complex.90.C2 pertType nd
set complex.90.C2 pertCharge -0.0693
                                                                     
                                                                     
   
set complex.90.H1 pertName LP
set complex.90.H1 pertType LP
set complex.90.H1 pertCharge -0.2255

...... (changing other charges in the residue)

saveAmberParmPert complex prmtop.uns prmcrd.uns

The prmtop.uns file produced doesn't contain any information about
perturbed bonds/angles/dihedrals
i.e.
%FLAG PERT_BOND_ATOMS
%FORMAT(10I8)
                                                                     
                                                                     
  
%FLAG PERT_BOND_PARAMS
%FORMAT(10I8)
                                                                     
                                                                     
  
%FLAG PERT_ANGLE_ATOMS
%FORMAT(10I8)
                                                                     
                                                                     
  
%FLAG PERT_ANGLE_PARAMS
%FORMAT(10I8)
                                                                     
                                                                     
  
%FLAG PERT_DIHEDRAL_ATOMS
%FORMAT(10I8)
                                                                     
                                                                     
  
%FLAG PERT_DIHEDRAL_PARAMS
%FORMAT(10I8)
                                                                     
                                                           
are all blank, but the PERT_ATOM_SYMBOL and PERT_CHARGE fields seem
to be fine.
The system runs apparently OK in sander with clambda = 0.5, but I'm
wondering if the blank fields should concern me. If so, how do I get
LeAP to fill them?

Thanks

Dave Evans
London School of Pharmacy
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu