Hello,
For one reason or another, 5' phosphate groups never made it into the
standard AMBER force field, so there is no automatic procedure for
generating one. I recall attempting to parameterize this myself via RED,
but I don't remember what came of it. In the end, it was much easier just
to neglect that group as it wasn't of particular interest in my case.
Regards,
Brian
On Tue, Sep 22, 2015 at 8:50 AM, Sidhu, Khushwant (Dr.) <
k.sidhu.leicester.ac.uk> wrote:
> Hi,
>
> I'm trying to model a protein-RNA complex and am getting the following
> error.
> The structure is from crystallography & RNA has a 5' phosphate group.
>
> A colleague of mine has used GROMACS with the charmm forcefield.
>
> cheers
>
> Sid
>
>
> (using default radius 1.500000 for P)
> (using default radius 1.500000 for OP1)
> (using default radius 1.500000 for OP2)
> (using default radius 1.500000 for P)
> (using default radius 1.500000 for OP1)
> (using default radius 1.500000 for OP2)
> Volume: 702281.164 A^3 (oct)
> Mass > 380261.604 amu, Density > 0.899 g/cc
> (type - hence mass - of one or more atoms could not be found)
> Added 19440 residues.
> > savepdb STAR-AUUAAA STAR-AUUAAA-BOX.pdb
> Writing pdb file: STAR-AUUAAA-BOX.pdb
> Converting N-terminal residue name to PDB format: NTYR -> TYR
> Converting C-terminal residue name to PDB format: CASP -> ASP
> Converting N-terminal residue name to PDB format: NTYR -> TYR
> Converting C-terminal residue name to PDB format: CPRO -> PRO
> > saveamberparm STAR-AUUAAA STAR-AUUAAA.top STAR-AUUAAA.crd
> Checking Unit.
> FATAL: Atom .R<A5 275>.A<P 32> does not have a type.
> FATAL: Atom .R<A5 275>.A<OP1 33> does not have a type.
> FATAL: Atom .R<A5 275>.A<OP2 34> does not have a type.
> FATAL: Atom .R<A5 281>.A<P 32> does not have a type.
> FATAL: Atom .R<A5 281>.A<OP1 33> does not have a type.
> FATAL: Atom .R<A5 281>.A<OP2 34> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
>
>
>
> ------------------------------------------------------------------------------------
>
> Dr Khushwant Sidhu
> Senior Experimental Officer / I. T. Professional
>
> Department of Molecular and Cell Biology,
> 1/61 Henry Wellcome Building , University of Leicester,
> Lancaster Road,
> Leicester,
> LE1 7RH
>
> T: 0116 229 7237
> E: k.sidhu.le.ac.uk<mailto:k.sidhu.le.ac.uk>
>
>
>
> _______________________________________________
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>
--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Tue Sep 22 2015 - 12:00:03 PDT
