AMBER Archive (2004)

Subject: Re: AMBER: Setting up thermodynamic integration

From: david.evans_at_ulsop.ac.uk
Date: Wed Sep 01 2004 - 12:24:40 CDT

Hi,

Partially solving my own problem, by tracing through the leap source
code, it seems
I should have used commands like

set complex.90.C2 pert true

for each atom I'm perturbing. I can't see this anywhere in the
manual, but perhaps I'm being blind.

Dave

---- Message from david.evans_at_ulsop.ac.uk at 2004-09-01 15:31:10
------
>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
>--------------------------------------------------------------------- 

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