Re: [AMBER] R.E.D, alkene isostere, Gly-Pro, P9501

From: FyD <>
Date: Fri, 10 Jan 2014 08:38:04 +0100

Dear Cecilia,

It looks like you study a bunch of different dipeptide analogs; you
could study all of them one by one using R.E.D. Server Dev. and then
once 'all' correctly defined you could rerun a job, which would
include all your dipeptide analogs, and generate an entire FF for all
these molecules _and_ fragments ready to be validated/used in MD
simulations. I would be happy if you would accept to submit this large
project in R.E.DD.B. once all fully defined.

I looked at your Gly-Pro analogs using:
  (x your cluster account; hidden for this email)

I am not a big fan ;-) of one atom type generated by R.E.D. Python in
this P9501 job: I would replace CA by CM in this case; we will correct
that; sorry for that...

A quick workaround until we correct this bug: just provide the full
list of FF atom types you want to use using:
MOLECULE1-ATMTYPE = your choice...

> I am trying to calculate charges for an alkene amide bond isostere
> for the dipeptide fragment Gly-Pro. By analogy I added the following
> information in a frcmod.user file:
> CM-CA-CT 70.0 119.70 Source (from CM-CM-CT)

as you can see you corrected by yourself ;-) CM-CA should be CM-CM

> CT-CA-CT 50.0 118.00 Source (from CT-N-CT)

for CT-CM-CT I would prefer to use CT-C -CT by analogy i.e. keeping
the same element; CM = C and not CM = N

> CA-CM-CT 70.0 119.70 Source (from CM-CM-CT)

will become CM-CM-CT and it is known

> C-CT-CA 63.0 110.10 Source (from C-CT-N)

same remark as above; and '63' could become '65'...

> CM-CT-N 63.0 110.10 Source (from C-CT-N)

same remark as above

More generally you could run R.E.D. Python using:
BASSET_OPTCALC = "6-311+G(d,p)"
to generate an optimized geometry generated using a larger theory
level and use ONLY the optimized geometry generated to ONLY determine
the equilibrium values of the unknown FF parameters listed in

> CM-CT-CA-CT 1.0 180.0 2 Source

i.e. will become CM-CT-CM-CT and consequently it should be found by
R.E.D. Python using X -X -CM-HA

> My question is: what information would you recommend that I use for
> IMPROPER: CM-CT-CA-CT? Here I have based it on C-CM-N*-CT, but I am
> not convinced that it is ok, but I have not found any other that I
> like better either... I am using amber99sb.

see above...

I hope this helps,
regards, Francois

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Received on Fri Jan 10 2014 - 00:00:02 PST
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