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
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Yongmei Pan
Sent: Friday, September 05, 2008 8:50 AM
To: amber.scripps.edu
Subject: AMBER: error when using tleap with leaprc.ff02EP
Hi, <mailto:amber.scripps.edu> 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.top x.crd
quit
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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Received on Sun Sep 07 2008 - 06:07:51 PDT
