Re: [AMBER] problem with parametrization of an organo-metallic cluster using RED server

From: FyD <>
Date: Thu, 17 Feb 2011 21:37:43 +0100

Dear Moitrayee,

> I am trying to get the FF for an organo-metallic moiety
> using RED server. I have successfully generated the p2n
> files using Ante_R.E.D. 2.0 and visualized the output in
> VMD. Things look alright.

I spent some time to figure out what was your private login...

I looked at your P2N file; this is a good starting point; three
comments however:

-1 Each amino-acid is represented by a NH-CH(R)-CO Central-fragment in
your input structure; this will generate problems during the geometry
optimization & MEP computation steps (see below the error message you
report); you need to start from a _whole_ molecule and your fragment
is simply built by using specific charge constraints during the charge

So you need to add ACE & NME capping groups in your molecule for each
amino-acid (although this is not be the best bet from our last tests).
Generate a correct!!! input geometry so that the QM geometry
optimization will not fail.
You can use the R.E.D. Server builder for that:

-2 I think you mixed up the HIE & HID residues (see the Amber force
field topology database) in your model; you have a N-H group that
points to the Cobalt atom which is bad; instead the non-bonding
electrons of N-: should point to the Co atom.

-3 Are you sure the Cobalt atom is penta-coordinated?

> However, when I submitted this p2n file for a geometry
> optimization using R.E.D. IV on the server (mode 1),
> I get the following error.


> Geometry optimization(s) is/are being computed for molecule 1 ...[FAILED]
> See the file(s) "JOB1-gau_m1-1.out"

If you look at the JOB1-gau_m1-1.out file, it is written:

The combination of multiplicity 1 and 375 electrons is impossible.

I think this QM error message should be printed in the R.E.D. log: we
will implement that soon. I hope this will help new users to quickly
understand such a problem.

This is normal because your input geometry corresponds to a molecular
fragment. Build a correct geometry/whole molecule, check the total
charge & spin multiplicity of your system and this will start. You
will have also to add INTRA-MCC keywords in your P2N file to define
the constraints used in the charge fitting step and consequently your

Finally last comments:

- You use the RESP-A1A charge model:
> ---------------------------
> * Welcome to R.E.D. IV *
> RESP ESP charge Derive
> Charge model RESP-A1A is compatible with the Cornell et al. force field.
> ---------------------------

I do not think RESP-A1A is the best choice in your case.

We have develop a new R.E.D. Server version that we call "R.E.D.
Server Development" .

The announcement of its release has been only carried out in the
q4md-fft mailing list since this server is still in development. The
new features of this server are:
- handling of ALL the elements of the periodic table (but a few elements).
- new charge models; up to 15 charge models by now.
- handling of automatic or specific atom radius in MEP computation for
metallic atoms.
- new resp version: resp version 2.2

See the faq of R.E.D. server development:
  & in particular:

I think you should use "R.E.D. Server development" & not "R.E.D.
Server" in particular when you wish to interface R.E.D; IV; then
select a better charge model (the user database for people that wish
to register is the same for the two R.E.D. Server versions).

New features to come pretty soon:
- new q4md-fft charge models for all the elements of the periodic table
- Ante_R.E.D. 2.1
- new algorithm to improve SCF & geometry convergence in the geometry
optimization step.
- full integration with R.E.DD.B.

If you want to use this new RESP version 2.2 on your workstation just
let me know, and we will release it on our q4md-fft web site...

I hope this helps.

regards, Francois

AMBER mailing list
Received on Thu Feb 17 2011 - 13:00:04 PST
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