Thanks! Switching to ff10 solved it.
I run into another issue with a Na+ ion because the ff10 leaprc file
includes ions08.lib but doesn't fully parametrize the ions defined
there. Very confusing -- because ions are correctly recognized but the
topology can then anyway not be saved. A water-model-specific mod
file needs to be loaded to finish the job. I see that this is supposed
to be feature rather than bug but then it would be much less
troublesome to either have a complete parametrization (by default for
TIP3) or have no ion definitions included at all.
Greetings,
Raik
On Wed, Nov 23, 2011 at 4:58 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>> ___________________________________
>>
>> _______________________________________________
>> AMBER mailing list
>> 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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>
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Received on Wed Nov 23 2011 - 21:30:03 PST
