[gmx-users] H211 in ffG53a5
Ken Rotondi
ksr at chemistry.umass.edu
Tue Apr 4 15:19:21 CEST 2006
Hi David,
Thanks for pursuing this,
No, unfortunately h211 is in neither the .hdb nor the .pdb file. I
attached the .pdb file to my first post as well as the additions I made
to the .hdb file. I've reattached them at the end of this post along
with the pdb2gmx error. I did in fact use the -ignh flag in pdb2gmx
although the .pdb file is w/out H's.
Is there a problem with the format of the .hdb (attached) changes I've
made? I would think not, since it removes the "warning, atoms etc. not
in .hdb file" problems, but you never know...
Could someone with other hardware/OS (I'm running on OS X.3.9/G3 and
RedHat/P4) run the test.pdb (1 nucleotide) with a .hdb file containing
the modifications to see if the problem is reproducible?
On Apr 3, 2006, at 5:26 PM, David Mathog wrote:
> Ken Rotondi wrote:
>
>
>> I've had this in AMBER for some time. I need to use a
>> UAFF.
>
> ok
>
>>>
>>> There is no H211 in either the .hdb or .pdb file.
>
> My first guess would be that even though you say it's not
> in there, it actually is. Perhaps it's in lower case and you
> used a case sensitive search? Try
>
> grep -i h211 *.hdb *.pdb
>
> and see if it turns up.
>
> -ignh might also be helpful (doubt it though). If all else fails
> backtrace through the code from the location of the error message
> until you find where that atom is coming from.
>
> Regards,
>
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
>
> _____________________
> ADE 3
> 1 2 H2* O2* C2* C3*
> 2 3 H61 N6 C6 N1
> 2 3 H62 N6 C6 N1
> GUA 4
> 1 2 H2* O2* C2* C3*
> 2 3 H21 N2 C2 N1
> 2 3 H22 N2 C2 N1
> 1 1 H1 N1 C6 C2
> CYT 3
> 1 2 H2* O2* C2* C3*
> 2 3 H41 N4 C4 N3
> 2 3 H42 N4 C4 N3
> URA 2
> 1 2 H2* O2* C2* C3*
> 1 1 H3 N3 C2 C4
> _____________________
>
> ATOM 1 P GUA A 1 4.006 48.703 126.810 1.00 58.91
> ATOM 2 O2P GUA A 1 4.598 50.201 126.810 1.00 58.91
> ATOM 3 O1P GUA A 1 3.130 48.474 125.479 1.00 58.91
> ATOM 4 O5* GUA A 1 5.220 47.646 126.843 1.00 58.91
> ATOM 5 C5* GUA A 1 6.464 48.349 126.894 1.00 58.91
> ATOM 6 C4* GUA A 1 7.236 48.051 128.158 1.00 58.91
> ATOM 7 O4* GUA A 1 7.567 46.637 128.194 1.00 58.91
> ATOM 8 C1* GUA A 1 8.854 46.462 128.764 1.00 58.91
> ATOM 9 N9 GUA A 1 9.716 45.855 127.755 1.00 58.91
> ATOM 10 C4 GUA A 1 10.914 45.215 127.975 1.00 58.91
> ATOM 11 N3 GUA A 1 11.509 45.032 129.173 1.00 58.91
> ATOM 12 C2 GUA A 1 12.655 44.380 129.062 1.00 58.91
> ATOM 13 N2 GUA A 1 13.383 44.113 130.156 1.00 58.91
> ATOM 14 N1 GUA A 1 13.174 43.942 127.869 1.00 58.91
> ATOM 15 C6 GUA A 1 12.580 44.119 126.624 1.00 58.91
> ATOM 16 O6 GUA A 1 13.135 43.683 125.607 1.00 58.91
> ATOM 17 C5 GUA A 1 11.350 44.818 126.728 1.00 58.91
> ATOM 18 N7 GUA A 1 10.447 45.200 125.746 1.00 58.91
> ATOM 19 C8 GUA A 1 9.496 45.810 126.400 1.00 58.91
> ATOM 20 C2* GUA A 1 9.338 47.838 129.227 1.00 58.91
> ATOM 21 O2* GUA A 1 8.990 48.036 130.582 1.00 58.91
> ATOM 22 C3* GUA A 1 8.576 48.757 128.282 1.00 58.91
> ATOM 23 O3* GUA A 1 8.414 50.063 128.828 1.00 58.91
> _____________________
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3
> Source code file: add_par.c, line: 221
>
> Fatal error:
> Atom H211 not found in rtp database in residue GUA, it looks a bit
> like H21
> -------------------------------------------------------
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