AMBER Archive (2008)

Subject: AMBER: error when using tleap with leaprc.ff02EP

From: Yongmei Pan (
Date: Fri Sep 05 2008 - 10:49:38 CDT

Hi, <> amber users

I tried to use tleap with leaprc.ff02EP.
the input file for tleap(AMBER8) is:

source leaprc.ff02EP
source leaprc.gaff
modf=loadamberparams *
loadamberprep *
pdb =loadpdb *
saveamberparmpol pdb x.crd

Then there are error warnings for every residue of pdb file:

There is a bond of 0.350000 angstroms between:
------- .R<NASP 1>.A<EP+1 15> and .R<NASP 1>.A<O 14>
There is a bond of 0.350001 angstroms between:
------- .R<NASP 1>.A<EP-1 16> and .R<NASP 1>.A<O 14>

I tryied leaprc.ff02 before. It goes smoothly. So who knows why there is
such error? thanks!

Yongmei Pan

Pharmaceutical sciences, University of Kentucky

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