AMBER Archive (2008)

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

From: Jacob Kongsted (Jacob.Kongsted_at_teokem.lu.se)
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 sanmin_com.in -o sander_com1.out -e mdenTTT -c btn1_tr_com.crd.1 -p compl_tr.prmtop

and hessian calculation:

nmode -O -i nmode_com.in -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
Sweden


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