igb=1 error message: Unable to find bonded partner for atom 239

From: Guanglei Cui <cuigl_at_morita.chem.sunysb.edu>
Date: Sat 9 Jun 2001 16:46:03 -0400

Dear Amber Users,
    I'm trying to do some GB calculation on a DNA system with a modified
base. After having gone through the setup stage, I'm ready to go. Xleap was
happy to generate the topology and coordinate file for me. However, it was
stucked in routine mdread.f when igb was set to 1. The error message was
shown in the subject area. This is particular to igb = 1. It doesn't happen
when it was switched to igb = 3. My question is how the array in mdread.f
resat organized and used here. It seems to me that the program assumes that
any hydrogen atoms are close to the heavy atoms they are bonded to (from the
do j = 1, 3 ...). Please let me know if my guess is right.


Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, Ny 11790
Received on Sat Jun 09 2001 - 13:46:03 PDT
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