AMBER Archive (2004)

Subject: AMBER: free energy perturbation questions

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Sat Apr 17 2004 - 09:38:28 CDT

Dear amber users£¬
        I want to calculate the binding free energy of a ligand to a protein(131 aa) by using free energy perturbation module.As instructed in tutorial,I changed the pert. name to DH and pert. charge to zero for all the atoms of ligand.In file frcmod,I added the following lines:
        previous frcmod file:
remark goes here
MASS

BOND
c2-ha 354.50 1.080 same as c2-hc

ANGLE

DIHE

IMPROPER
c2-c3-c2-ha 1.1 180.0 2.0 Using default value

NONBON

the modified frcmod file :
remark goes here
MASS
DH 1.0(or 0)

BOND
c2-ha 354.50 1.080 same as c2-hc
DH-DH 0 1.000(or 0)

ANGLE
DH-DH-DH 0. 0.

DIHE
DH-DH-DH-DH 1 0.0 0. 1.
   
IMPROPER
c2-c3-c2-ha 1.1 180.0 2.0 Using default value
DH-DH-DH-DH 1.1(or 0) 180.0(or 0) 2.0(or 0)

NONBON
  DH 0.0 0.0
   when I tryed to save topology file and crd file.
   following errors were displayed on the screen:
Please add a dummy parameter of multiplicity 2
for the pert types to your parameter set.
 - e.g. DH-DH-DH-DH 1 0.0 0. 2.
(This is because multiple torsional potentials may apply to a
single torsion, and each is perturbed individually in gibbs.)
*** Proper torsion parameters missing ***
 atom names: O1-C2-C1-H1
 atom types: oh-c-c3-hc =pert=> DH-DH-DH-DH
Please add a dummy parameter of multiplicity 1
for the non-pert types to your parameter set.
 - e.g. oh-c-c3-hc 1 0.0 0. 1.
(This is because multiple torsional potentials may apply to a
single torsion, and each is perturbed individually in gibbs.)
*** Proper torsion parameters missing ***
 atom names: O1-C2-C1-H1
 atom types: oh-c-c3-hc =pert=> DH-DH-DH-DH
Please add a dummy parameter of multiplicity 2
for the pert types to your parameter set.
   why? what should I add to file frcmod ?How to determine the values of MASS ,BOND,DIHEDRAL parameters?
   Can anyone give me some suggestions?
   Thank you in advance.

best regards

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