AMBER Archive (2008)

Subject: AMBER: ff02 in nmode gives error "too many dihedrals" ?

From: Jacob Kongsted (
Date: Mon Nov 10 2008 - 03:16:36 CST

Dear Ambers,

Im am doing minimization using sander and ff02. After the minimization I would like to enter the nmode part of the code in order to do a vibrational analysis in order to get estimates of the vibrational entropy. The sander minimization runs fine, but upon entering nmode I get the following error meassage:

"too many dihedrals"

This error related to the load14 routine in rdparm.f and connects to the istuff routine in the same file.

I cannot understand this error meassage and indeed if I dress the molecular configuration with a nonpolarizable ff, i.e. ff94, I do not see the same error but everything runs fine. Also, I can use ff02 and put ipol = 0 and nmode does not give me any problems. So this error seems to be specifically related to inclusion of polarization. Obviously, I would say that the number of dihedrals should, for a given molecular configuration, be independent of the force-field used.

I have attached the relevant files in a zipped tar file.

These can be executed by (minimization):

sander -i -o sander_com1.out -e mdenTTT -c btn1_tr_com.crd.1 -p compl_tr.prmtop

and hessian calculation:

nmode -O -i -o nmode_compl1.out -c restrt -p compl_tr.prmtop

As said, the first one runs fine while the problem show up in the latter run.

I use Amber8 but have also tested this with Amber9 and get the same error.

Can anybody help me on this?

Best, Jacob.

Jacob Kongsted
Department of Theoretical Chemistry
University of Lund
Chemical Centre, P. O. Box 124
S-221 00, Lund

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