Is this the recent git checkout or amber11/ambertools1.4? As I recall, I
had a similar issue that Wei fixed via a bugfix.
On Mon, Aug 30, 2010 at 9:26 PM, Ben Roberts <roberts.qtp.ufl.edu> wrote:
> Hi,
>
> Yet another sleap oddity this evening. I discovered that sleap complains
> about addions.
>
> Say I want to add a sodium ion to a C-terminal methionine (this PDB):
>
> ATOM 1 N MET 1 100.638 77.098 91.233 1.00 0.00
> N
> ATOM 2 CA MET 1 99.570 77.610 92.126 1.00 0.00
> C
> ATOM 3 C MET 1 98.393 76.645 92.225 1.00 0.00
> C
> ATOM 4 O MET 1 97.955 76.363 93.338 1.00 0.00
> O
> ATOM 5 CB MET 1 99.011 78.975 91.714 1.00 0.00
> C
> ATOM 6 CG MET 1 99.936 80.170 91.929 1.00 0.00
> C
> ATOM 7 SD MET 1 99.055 81.757 91.888 1.00 0.00
> S
> ATOM 8 CE MET 1 98.262 81.701 90.261 1.00 0.00
> C
> ATOM 9 OXT MET 1 97.383 76.550 91.460 1.00 0.00
> O
> ATOM 18 H MET 1 101.503 77.602 91.355 1.00 0.00
> H
> ATOM 10 HA MET 1 99.973 77.689 93.135 1.00 0.00
> H
> ATOM 11 HB2 MET 1 98.698 78.942 90.671 1.00 0.00
> H
> ATOM 12 HB3 MET 1 98.134 79.156 92.331 1.00 0.00
> H
> ATOM 13 HG2 MET 1 100.411 80.081 92.905 1.00 0.00
> H
> ATOM 14 HG3 MET 1 100.708 80.172 91.163 1.00 0.00
> H
> ATOM 15 HE1 MET 1 97.797 82.665 90.055 1.00 0.00
> H
> ATOM 16 HE2 MET 1 99.015 81.488 89.504 1.00 0.00
> H
> ATOM 17 HE3 MET 1 97.495 80.927 90.241 1.00 0.00
> H
> END
>
> Using this leaprc:
>
> source leaprc.ff99SB
> model = loadpdb methionine.pdb
> addions model Na+ 1
> saveamberparm model BPR-20100830-003_out.parm7 BPR-20100830-003_out.rst7
> savePdb model BPR-20100830-003_out_leap.pdb
> quit
>
> I get this message:
>
> [gtkleap]$ addions model Na+ 1
> Assertion failed: (absid >=0 && absid < m_idcounter), function get_sptr,
> file data.cpp, line 442.
> Abort trap
>
> Using a much larger protein, the addions step is passed, but saveamberparm
> causes a problem:
>
> [gtkleap]$ saveamberparm model BPR-20100830-002_out.parm7
> BPR-20100830-002_out.rst7
> Assertion failed: (key.size() == value.size()), function sort_key, file
> exclude.cpp, line 54.
> Abort trap
>
> In conjunction with solvation beforehand (solvateOct), I get a segmentation
> fault instead.
>
> I may have a poke around in the code to see what's going on. However, I'd
> welcome any help from others who have seen the same thing.
>
> Cheers,
> Ben
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Aug 31 2010 - 07:00:04 PDT
