Re: [AMBER] Error while running tleap for protein-RNA complex

From: Shreeramesh <>
Date: Tue, 12 May 2015 02:48:47 -0700

Dear Hector and David,

Thanks for your valuable suggestions. I added the TER card between missing
residues in protein (rec1.pdb) and RNA (rec2.pdb). I also changed the
residue names CYS to CYX. It helped to fix the angle parameter for SH.
However, the following error remains.

Can you please help me to solve? and kindly let me know about the
generation of appropriate library unit for 5' phosphate

I also have attached the tleap script as well as pdbs in attachments for
your kind attention


Checking Unit.
FATAL: Atom .R<RG5 556>.A<OP2 35> does not have a type.
FATAL: Atom .R<RG5 556>.A<OP1 34> does not have a type.
FATAL: Atom .R<RG5 556>.A<P 33> does not have a type.
FATAL: Atom .R<RC5 591>.A<OP2 32> does not have a type.
FATAL: Atom .R<RC5 591>.A<OP1 31> does not have a type.
FATAL: Atom .R<RC5 591>.A<P 30> does not have a type.
Failed to generate parameters
Parameter file was not saved.

Thanks & regards

*Dr. Ramesh M*
Mobile: (91) + 9646469938 (27) + (0) 844556164

On Mon, May 11, 2015 at 4:55 AM, David A Case <>

> On Mon, May 11, 2015, Shreeramesh wrote:
> >
> > WARNING: There is a bond of 7.165783 angstroms between:
> > ------- .R<LEU 358>.A<C 18> and .R<LYS 359>.A<N 1>
> You'll have to examine your starting structure to figure out the origin of
> warnings like these...are there missing residues in your protein?
> > Could not find bond parameter for: SH - SH
> This is probably because you have CYS residues in your protein that should
> be
> CYX. A simple approach is to use the pdb4amber script on your input pdb
> file
> before loading it into tleap.
> > FATAL: Atom .R<RG5 170>.A<P 33> does not have a type.
> The 5' residues in Amber do not have a terminal phosphate, but this group
> is
> apparently present in your input pdb file. There is hence a mismatch
> between
> the library and your input pdb, which needs to be resolved, either by
> removing
> the phosphate group from the pdb file, or by generating an appropriate
> library
> unit.
> [There may(?) already be such a unit in the RED database. In any event,
> some
> enterprising developer should make it easier to handle these 5' phosphates,
> since they come up reasonably often.]
> ....dac
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Received on Tue May 12 2015 - 03:00:02 PDT
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