Hi,
If you haven't already, I recommend you read section 6.8 of the
AmberTools manual (Preparing PDB Files), which has helpful advice on
how to prepare PDBs for LEaP.
On Sat, Nov 16, 2013 at 2:17 PM, Helen Lvy <helenyuan0302.outlook.com> wrote:
> however, it seems something is going wrong, because it keeps showing:
>
>
>
>>Warning: name change in pdb file residue 1;
>
>> this residue is split into OL and PC.
This warning just means that you have ATOM records with the same
residue number but different residue name, so LEaP is splitting them
into two separate residues. This is only a problem if you don't have
residue libraries for OL and PC.
>>Created a new atom named: HT1 within residue: .R<NASN 1>
>
>>Created a new atom named: HT2 within residue: .R<NASN 1>
>
>> Fatal: Atom .R<NASN 1>. does not have a type.
This has been discussed on the list before (see e.g.
http://archive.ambermd.org/201306/0730.html). I find it best in such
cases to just remove the 'H' atoms from the PDB and let LEaP build
them back in from residue templates. Be aware that the default
N-terminal amino acid residue templates in Amber are protonated (it
appears from the naming scheme that in your PDB the N-terminal ASN may
be neutral).
Hope this helps,
-Dan
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Nov 18 2013 - 09:30:03 PST
