amber-developers: Problem in xleap

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Wed, 28 Mar 2007 19:57:25 -0400 (EDT)

Dear All,

In AMBER 8, I do not have the problem that I will be describing shortly. I
have a .prepi file and frcmod file for HEME structure (I cannot recall
from where I got it). When I load these files into leap and when I try to
create the prmtop/inpcrd files, I am getting the following error message
(I have attached the files that I am using):

-------------------------------------------------------------
# xleap -f xleap1.in
.
.
.
.
.
Building topology.
Building atom parameters.
For atom: .R<HEM 1>.A<NA 2> Could not find type: NP
For atom: .R<HEM 1>.A<CBB 45> Could not find type: CX
For atom: .R<HEM 1>.A<NB 48> Could not find type: NO
For atom: .R<HEM 1>.A<CBC 55> Could not find type: CX
For atom: .R<HEM 1>.A<NC 58> Could not find type: NP
For atom: .R<HEM 1>.A<ND 72> Could not find type: NO
Parameter file was not saved.
-------------------------------------------------------------

When I modify the frcmod file and add 3 more lines to the end of frcmod
file (which is the NONBON part), everything works fine:

-------------------------------------------------------------
# xleap -f xleap2.in
.
.
.
.
.
 <HEM 1>: C3D C4D C2D CAD
 <HEM 1>: C4A NA C3A CHB
 <HEM 1>: C4B NB C3B CHC
 <HEM 1>: C4C NC C3C CHD
 <HEM 1>: C4D ND C3D CHA
 total 22 improper torsions applied
 20 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
-------------------------------------------------------------

Those 3 lines are just 3 NONBON terms (zero):

NONBON
  FE 1.20000 0.05000 0.00000
  LO 1.60000 0.20000 0.00000
  LC 1.85 0.12 0.0
  NP 0.00000 0.0000 0.00000
  NO 0.00000 0.0000 0.00000
  CX 0.00000 0.0000 0.00000

In AMBER 8, I do not have this problem. Moreover, It gives error for the
atom types NP,NO,CX; not for the other ones (There are total 8 new atom
types defined in the frcmod file).

Does this sound like a bug, or am I missing something here? Thanks in
advance.

Best,

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------







Received on Sun Apr 01 2007 - 06:07:17 PDT
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