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.
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Dr Khushwant Sidhu
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Department of Molecular and Cell Biology,
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Received on Tue Sep 22 2015 - 07:00:04 PDT
