AMBER Archive (2004)

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

From: Carsten Detering (detering_at_u.washington.edu)
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
message:

> 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 

-- 

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

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