Re: [AMBER] problem with resp charge generation with multiple orientations

From: FyD <>
Date: Fri, 10 Dec 2010 17:13:40 +0100

Dear Thomas,

> For the gaussian calculations i used the R.E.D Server and i compared my
> files with your files given below:
> The espot_m1* files look from the format the same, and in the
> concatenated one there are no blanc lines.


> The input1_m1 / input2_m1 file also look similar (only the last
> paragraph differes because i have 4 and here in the example are 2
> orientations).


> When i use espot_m1 as an input for respgen / resp of AMBER i get the
> same problem as before (resp charges correspond to the first molecule of
> the esp-data).
> So it seems to me that the problem lies somewhere in the protocol i used
> for the AMBER stuff.


> With the resp charges of the R.E.D. Server (in Mol_m1-o1.mol2) i have
> the following problem:
> My molecule is mesitylene.

so this isésitylène right ?

> The charges of the hydrogen in the
> methyl-groups are the same (for each group), but all other charges
> differ by each other. Since the molecule is symmetric the charges of all
> 3 methyl-groups should be the same.


> In your Ethane-1,2-diol example this is not the case (the charges are
> symmetric, how they should be). Am i missing somewhere a flag or
> otherstuff, so that the R.E.D. Server recorgnises the symmetrie of the
> molecule and makes the resp-charges also symmetric?

Chemical equivalencing is defined by Ante_R.E.D. 2.0. in R.E.D. Server
- bugs are always possible since Ante_R.E.D. 2.0 is quite new - We
have already corrected many problems ;-)

-1 I just built Mesitylene using the new Java applet for R.E.D. Server
directly from Toluene... See

-2 then, I ran Ante_R.E.D. 2.0 for Mésitylène; chemical equivalencing
seems ok to me in the three cases below:
   or (different
   or (different tree

-3 then, I ran R.E.D. IV using Firefly (since I used the public
account to share data)

charge derivation data are .
   mol2 file is .
=> charge equivalencing is correctly performed.
  & inputs are correct i think

please tell me if I missed something...

regards, Francois

PS Then if you want to involve this building block in some
macrostructure building you will have to break the chemical
equivalencing defined by Ante_R.E.D. 2.0...

AMBER mailing list
Received on Fri Dec 10 2010 - 08:30:02 PST
Custom Search