Try using ff99SB (which is the protein force field part of ff10, which is
the version I would actually suggest using). Despite its label, it is
actually a 2006 update of the ff99 force field which performs at least as
well (if not better) as ff03. Indeed, there is no C-terminal CYX residue
defined in all_aminoct03.lib, but there is one in aminont10.lib (which
means it will work for FF10 in AmberTools 1.5).
HTH,
Jason
On Wed, Nov 23, 2011 at 4:13 PM, Raik Grünberg <raik.gruenberg.gmail.com>wrote:
> 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
>
>
>
>
>
>
> --
> --
> ___________________________________
> Raik Grünberg
> http://www.raiks.de/contact.html
> ___________________________________
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Nov 23 2011 - 14:00:03 PST
