Hi,
I am trying to build a topology for a protein with a C-terminal Cys
involved in a disulfide bond. The residue is named 'CYX' and I run the
following tleap script:
source /usr/local/lib/amber11/dat/leap/cmd/leaprc.ff03.r1
p = loadPdb /tmp/tmpu35bZfleap_in0.pdb
The leap output at this point is:
Loading PDB file: /tmp/tmpu35bZfleap_in0.pdb
Unknown residue: CCYX number: 55 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: CYX sequence: 56
...
and from there on everything goes wrong of course.
I think this used to work with Amber 8 and the ff99 forcefield but I
haven't got any Amber 8 installation running anywhere so I cannot be
sure. Could also be that I simply never tried this before. The
internal CYX residues are recognized perfectly. This is how the end of
the PDB looks like
ATOM 842 N CYX 56 18.647 36.632 30.550 0.00 0.00 N
ATOM 843 H CYX 56 18.553 36.474 29.557 0.00 0.00 H
ATOM 844 CA CYX 56 19.158 37.911 30.996 0.00 0.00 C
ATOM 845 HA CYX 56 19.793 37.747 31.866 0.00 0.00 H
ATOM 846 CB CYX 56 19.977 38.634 29.923 0.00 0.00 C
ATOM 847 HB2 CYX 56 19.462 38.565 28.964 0.00 0.00 H
ATOM 848 HB3 CYX 56 20.093 39.682 30.198 0.00 0.00 H
ATOM 849 SG CYX 56 21.520 37.867 29.363 0.00 0.00 S
ATOM 850 C CYX 56 17.841 38.672 31.206 0.00 0.00 C
ATOM 851 O CYX 56 16.761 38.107 31.044 0.00 0.00 O
ATOM 852 OXT CYX 56 17.850 39.855 31.538 0.00 0.00 O
TER 852 CYX 56
ATOM 853 Na+ Na+ 57 24.745 43.506 22.416 0.00 0.00 N
END
Any ideas what I am doing wrong?
Many thanks in advance!
Raik
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Raik Grünberg
http://www.raiks.de/contact.html
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Received on Wed Nov 23 2011 - 13:30:02 PST
