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
[EMAIL PROTECTED]
Manager, Sequence Analysis Facility, Biology Division, Caltech
_____________________
<x-tad-smaller>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
_____________________</x-tad-smaller>
<x-tad-smaller>-------------------------------------------------------
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
-------------------------------------------------------
</x-tad-smaller>
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