Hi Ying,
The "nt" and "ct" in the file names refer to "N-terminal" and "C-terminal."
In ff03, residues at the termini are still treated with the old parm94
charges, but all the internal residues are treated with new charges. The
mixing of charge derivations for these residue types is usually fine, but it
may not be for your system. See this thread for more discussion:
http://archive.ambermd.org/200608/0049.html
Steve
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
WANG,YING
Sent: Tuesday, October 23, 2007 12:08 PM
To: amber.scripps.edu
Subject: Re: AMBER: question about charge of prmtop file
Hi, Thanks very much!!
Could I ask another question about the .in files? When I load
leaprc.ff03, the xleap tell me that all amino03.in,
allaminoct94.in and all aminont 94.in are loaded. So when I use
"saveamberparm" to generate the .prmtop file, which .in file will
be use as template? I guess that it should be all amino03.in as
the manual told. But what the all_aminoct94.in and all_aminont
94.in use for? I'm confused about that...............
Thanks very much!!
Ying
On Tue Oct 23 11:41:09 EDT 2007, Thomas Steinbrecher
<steinbrt.scripps.edu> wrote:
> Hi Wang,Ying,
>
> the atomic charges in the prmtop file are the partial charges
> multiplied by 18.2223. This is done for performance I guess and
> one of the reasons why I refer to the prmtop files as almost
> human-readable. See also
>
> http://amber.scripps.edu/Questions/units.html
>
> Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
>
> On Tue, 23 Oct 2007, WANG,YING wrote:
>
>> Hi, Dear all,
>> I have a question about the unit of the charge values of the
>> atoms of the .prmtop file. Could any body tell me what's the
>> unit? It is not e.u. and it also doesn't look like coulomb.
>> Thanks very much!!
>>
>> Have a good day!
>>
>>
>>
>>
>>
>>
>> --
>> WANG,YING
>>
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--
WANG,YING
Mechanical and Aerospace Engineering
University of Florida
Office: NEB 139
TEL: 001-352-846-3030
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Received on Sun Oct 28 2007 - 06:07:08 PDT
