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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Received on Fri Dec 05 2008 - 14:07:44 PST
