Re: [AMBER] Resp charges for large number of atoms in an ONIOM calculation

From: Hamed S. Hayatshahi <>
Date: Tue, 16 Jul 2013 09:48:27 -0700 (PDT)

Dear Morteza;

In addition to what Francois mentioned, I remember that I had similar experience with resp and R.E.D. script and eventually the problem was from the maxq, maxlgr and maxmol values in the "$AMBERHOME/AmberTools/src/etc/limits.h". You may need to increase the those values and reconfigure. 
I hope this will help.
Hamed S. Hayatshahi
Graduate Student of Medicinal Chemistry
University of Utah
+1 (801) 807 4121


 From: FyD <>
To: AMBER Mailing List <>
Sent: Tuesday, July 16, 2013 7:13 AM
Subject: Re: [AMBER] Resp charges for large number of atoms in an ONIOM calculation

Dear Morteza Chehel Amirani,

> I have a problem in Resp charge calculation using antechamber. I have an
> ONIOM (QM:Amber) file generated in Gaussian and there are around 150 atoms
> in  the QM layer and 1000 atoms in the MM layer. To get Resp charges, I get
> gesp file using Gaussian but when I use this file in antechamber to
> generate Resp charges, I get an error indicating that antechamber can not
> deal with this number of atoms. I'm wondering if there is any way to
> calculate Resp charges for this system. Any help is appreciated.

In general one derives RESP charge values for small molecules; charges 
for biopolymers are obtained from the repetition of molecular 
Moreover I am not sure how is treated chemical equivalencing in this 
type of large molecular systems; I guess it is simply not considered 
making the approach even more suspicious; just my personal opinion ;-)

If you want to derive RESP charges and build force field libraries for 
molecular fragments you might be interested by R.E.D. Server; see 

regards, Francois

AMBER mailing list
AMBER mailing list
Received on Tue Jul 16 2013 - 10:00:02 PDT
Custom Search