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):
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# 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.
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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:
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# 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)
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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/ -
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Received on Sun Apr 01 2007 - 06:07:17 PDT
