AMBER Archive (2004)

Subject: AMBER: TI, angle parameters for nitrogen, frcmod

From: Carsten Detering (
Date: Mon Feb 02 2004 - 14:38:59 CST

Hi all,

I am trying to set up a thermodynamic integration calculation, in which
I want to change a CH3 in to a NH2. I edit the atoms such that the c3
becomes an n3, hc becomes hn and one hc becomes a dummy atom.
However, when I want to save the amberpert file, I get the error message
that the torsion parameters are missing; although I have edited the
frcmod file according to xleaps suggestions, I keap getting the same

> saveamberparmpert bw_solv bw_pert.prmtop bw.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
*** Improper torsion parameters missing ***
  atom names: NB-C31-CA1-NA
  atom types: nb-c3-ca-n =pert=> nb-n3-ca-n
Please add a dummy parameter of multiplicity 2
for the pert types to your parameter set.
  - e.g. nb-n3-ca-n 0.0 0. 2.
(This is because multiple torsional potentials may apply to a
single torsion, and each is perturbed individually in gibbs.)
old PREP-specified impropers:
  <* 1>: CA8 CA6 CA7 H8
  <* 1>: CA7 CA5 CA6 H7
  <* 1>: CAD CA6 CA5 CA4
  <* 1>: CA3 CA5 CA4 H6
  <* 1>: CA2 CA4 CA3 H5
  <* 1>: CA3 CAC CA2 NB
  <* 1>: C31 NA CA1 NB
  <* 1>: C4 CA1 NA H1
  <* 1>: CAC NA C4 O6
  <* 1>: C4 CA2 CAC CAD
  <* 1>: CAC CA9 CAD CA5
  <* 1>: CAD CA8 CA9 H9
  <* 1>: C32 CA9 CA8 CA7
  <* 1>: C32 CAE N31 H12
  <* 1>: CAJ CAF CAE N31
  <* 1>: CAE CAI CAJ H15
  <* 1>: CAJ CAH CAI H14
  <* 1>: CAE CAG CAF H13
  <* 1>: C33 CAF CAG CAH
  <* 1>: C5 CAI CAH CAG
  <* 1>: CAH N32 C5 O4
  <* 1>: C34 OH1 C6 O5
  <* 1>: C37 O6 C7 OH2
  total 24 improper torsions applied
  23 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.

How can I avoid this message, respectively how would I have to edit the
frcmod file? I noticed that the format is

n-ca-n3-DH 1 0.0 0. 2.

but that the "1" is missing in the suggested dummy parameter.

Any helpful suggestions will be appreciated.

Thanks in advance,



Carsten Detering University of Washington Seattle, WA 98195 Fon 206.543.5081 Fax 206.685.8665

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