Re: amber-developers: Problem in xleap

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Thu, 29 Mar 2007 00:20:07 -0400 (EDT)

I figured out that the file parm.dat was changed in some places.

660,661c673,674
< N NA N2 N* NC NB NT NP NO NY
< C* CA CB CC CD CK CM CN CQ CR CV CW CX CY CZ
---
> N   NA  N2  N*  NC  NB  NT  NY
> C*  CA  CB  CC  CD  CK  CM  CN  CQ  CR  CV  CW  CY  CZ
I am not sure how to include this info in a frcmod file. In any case, I
received an email from someone saying that he could not load the HEM
parameter files. I wonder why this part of the parm99.dat file was
changed.
Best,
On Wed, 28 Mar 2007, Ilyas Yildirim wrote:
> 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      -				-
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  - 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 - 06:07:19 PDT
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