AMBER Archive (2004)

Subject: AMBER: parametrization problem

From: Carsten Detering (detering_at_u.washington.edu)
Date: Fri Jul 23 2004 - 13:16:13 CDT

Dear Ambers,

I was loading an off-file into xleap for a complex that I previously had
successfully saved as a paramterfile for sander. Leap was started with
'xleap -s -f leaprc.ff99', so all the parameters should be loaded.
However, when I want to save the paramter file, I get the error message:

-- Building topology.
Building atom parameters.
For atom: .R<GLY 29>.A<HA2 4> Could not find type: H0
For atom: .R<GLY 29>.A<HA3 5> Could not find type: H0
For atom: .R<GLY 35>.A<HA2 4> Could not find type: H0
For atom: .R<GLY 35>.A<HA3 5> Could not find type: H0
For atom: .R<GLY 44>.A<HA2 4> Could not find type: HO
....
For atom: .R<GLY 253>.A<HA3 5> Could not find type: H0
For atom: .R<GLY 300>.A<HA2 4> Could not find type: H0
For atom: .R<GLY 300>.A<HA3 5> Could not find type: H0
Parameter file was not saved.

How come that it assigns type HO to these two atoms?
I didnt change anything neither in the leaprc file, nor the off file.

Thanks for helpful suggestions.

Carsten. 

--
Carsten Detering
University of Washington
Seattle, WA 98195
Fon 206.543.5081
Fax 206.685.8665

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