Hi, Thanks very much!!
So, as my understanding, in amber, when I use ff03, all the
internal residues are treated with all_aminoacid03.in parameter
but the termial residues are treated with "ct94" or "nt94". Is it
right?
Really really thanks for your reply!
Ying
On Wed Oct 24 10:21:25 EDT 2007, Steve Spronk <spronk.umich.edu>
wrote:
> 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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--
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 - 06:07:09 PDT
