On Mon, Jun 13, 2016 at 4:11 AM, Shreeramesh <shreeramesh.gmail.com> wrote:
> Can you please let me know where I can find the AMBER residue names and
> atom types for all the amino acids?
With a few exceptions, Amber uses the PDB V3 standard names for
residues and atoms. As Dave mentioned, if you want to know the names
for a particular residue you can look at them in LEaP with the 'desc'
command, e.g.
tleap -f leaprc.protein.ff14SB
desc CGLU.1
-Dan
>
>
> Thanks & regards
>
> *Dr. Ramesh M*
>
> Email: shreeramesh.gmail.com
> Mobile: (91) + 9646469938 (27) + (0) 844556164
>
>
>
> On Sat, Jun 11, 2016 at 10:20 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Fri, Jun 10, 2016, Shreeramesh wrote:
>> >
>> > Checking Unit.
>> > FATAL: Atom .R<CGLU 349>.A<OCT2 18> does not have a type.
>> > FATAL: Atom .R<CGLU 349>.A<OCT1 17> does not have a type.
>>
>> You pdb file contains non-standard atom names. The carboxylic oxygens
>> on a C-terminal residue need to be named "O" and "OXT". Edit the pdb file
>> to change these.
>>
>> To find this out for yourself, use the "desc" command in tleap to see what
>> atom names are in the CGLU unit: you pdb file has to match these.
>>
>> ....dac
>>
>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Jun 13 2016 - 08:00:02 PDT
