Re: [AMBER] Probelm with antechamber for resp charge derivation

From: FyD <>
Date: Wed, 25 Sep 2013 11:27:42 +0200

Dear Fengxue Li,

Deriving charges for a large molecule likely means you do not control
the conformation of this molecule. As conformation strongly affects
charge values I like to control the conformation(s) involved in charge
derivation; i.e. deriving charges for a large molecule is
'arguable'... Thus, I would like to suggest you to split your large
molecule - 130 atoms is a looooot ;-) into elementary building blocks,
and consequently to use R.E.D. Server.
See for instance:

A side effect for large molecules is that the program executed cannot
handle the input molecule. A problem we have encountered in the
development of R.E.D. Python is how building an algo. for calculating
chemical equivalencing of charge values for large molecules (that
cannot be split into building blocks because of electron
delocalization) and/or molecules with multiple cycles. A consequence
here is that the amount of required memory can drastically increased,
and it looks like this is what appends in your case; I guess you could
modify in the Antechamber source code the amount of memory, but the
code will crash again for sure for a slightly more complex problem;
this is a ever ending problem...

My conclusion: Just learn the building block approach, and use R.E.D.
Server; then send a request to the private assistance service to ask
for post-precessing your data with our new R.E.D. Python code (until
it is available) so that you end up with a project with atom types &
frcmod files...

regards, Francois

> I used antechamber implemented in AMBER11 package to derive Resp
> charge for a molecule. Its consists of 132 atoms, and a net charge
> of 0. I followed the following procedures to derive resp charge:
> [1] Optmized at HF/6-31g* and did single point energy calculations
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/41=10) iop(6/42=8)
> [2] Then i used antechamber the following command to derive resp
> charge
> antechamber -i name.log -fi gout -o name.prepi -fo prepi -c resp -s 2
> I got these informations when the job was running
> Info: the number of the path atoms exceeds MAXPATHATOMNUM(10000)
> for atom[109],extend the size and reallocate the memory automatically
> and in the end no error, it will creat the required resp input
> file for my molecule (name.prepi)
> I want to know the resons for this situation ,like this infomation :
> Info: the number of the path atoms exceeds MAXPATHATOMNUM(10000) for
> atom[109],extend the size and reallocate the memory automaticall
> Can anyone help me?

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Received on Wed Sep 25 2013 - 02:30:02 PDT
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