AMBER Archive (2008)

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

From: Ross Walker (
Date: Fri Sep 05 2008 - 11:06:13 CDT

Hi Yongmei,


Assuming all the warnings are for EP (extra point) atoms you can safely
ignore them. Leap here wasn't set up to recognize that extra points are
special and so a bond of 0.35 angstroms to one of them is not a problem.


All the best



From: [] On Behalf Of
Yongmei Pan
Sent: Friday, September 05, 2008 8:50 AM
Subject: AMBER: error when using tleap with leaprc.ff02EP


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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