In addition to Jasons comments, check out this recent paper on the
thinking behind the phosphotyrosine parameters, which build on the work
that Anselm has cited:
http://pubs.acs.org/doi/abs/10.1021/ct300613v
Thomas
On Mon, October 29, 2012 11:05 am, Jason Swails wrote:
> The problem here is that your phosphotyrosine connects to residues on
> either side of it. As a result, there are bonds between atoms in your
> phosphotyrosine (whose atom types are gaff atom types) and atoms in the
> rest of your protein (whose atom types are Amber atom types). Since these
> bonds (and corresponding angles and dihedrals) do not appear in your TRS
> residue, parmchk does not know to look for them (nor could it find them).
>
> This is why you are getting these errors. For phosphotyrosine, your
> residue really should be typed like the AMBER force fields, not like the
> gaff force field. You can do this via the "-at amber" flag in antechamber
> (run antechamber with no arguments to get the full usage).
>
> However, you should carefully check that the atom types in your residue
> matches the atom types in the normal tyrosine residue where appropriate.
>
> However, AmberTools 12 includes a library file with phospho-amino acids
> (among them phosphotyrosine (-2), phosphoserine (-2), phosphothreonine
> (-2), phosphohistidine (-2), phosphotyrosine (-1), phosphoserine (-1), and
> phosphothreonine (-1). See $AMBERHOME/dat/leap/lib/phosphoaa10.lib and
> the
> corresponding phosphoaa10.readme file that has the information as well as
> the published reference with the parametrization.
>
> Unless you are interested in going through the exercise as an example, I
> would suggest using these parameters instead.
>
> Good luck,
> Jason
>
> On Mon, Oct 29, 2012 at 10:46 AM, PAUL NEWMAN <paulclizana.gmail.com>
> wrote:
>
>> Hello Anselm,
>>
>> Thanks for fast reply. I am not an expert building force fields, and yes
>> I
>> am doing it just because I need it. Could you please be more especific?
>>
>> I compared the lib files and it looks that they are consistent. However
>> there is no FRCMOD files availables to compare.
>>
>> Please any expert building force field that can point out what is wrong;
>> I
>> will highly appreciate it.
>>
>>
>> Thanks
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Oct 29 2012 - 11:30:05 PDT
