On Mon, 2014-09-29 at 19:08 +0530, Vishal Nemaysh wrote:
> *Dear all, I am getting a error leap when i prepare the .prmtop & .inpcrd
> files. How to resolve it? the pdb file is also attached herewith. Thanks in
> advance*
>
>
> *> saveamberparm dna dna_wat.prmtop dna_wat.inpcrd*
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -23.000000 is not zero.
> FATAL: Atom .R<DG5 1>.A<H 32> does not have a type.
> FATAL: Atom .R<DG 4>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 7>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 10>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 13>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 16>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 19>.A<H 34> does not have a type.
> FATAL: Atom .R<DG 22>.A<H 34> does not have a type.
I'm not sure where you got this PDB file from, but the atom names are
non-standard. In particular, the hydrogen atoms seem to have the wrong
names (they have to match up with the atom names in the residue template
libraries in $AMBERHOME/dat/leap/lib).
You can get around this issue by deleting all of the Hydrogen atoms from
your PDB file -- you can do this with the command:
reduce -Trim dna.pdb > dna_noh.pdb
After this, dna_noh.pdb will work with tleap, but you should check to
make sure that all of the Hydrogen atoms added by tleap look reasonable.
They usually are in my experience, but you can use "reduce" to get
better hydrogen placement as well.
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 29 2014 - 07:30:02 PDT
