AMBER Archive (2006)

Subject: Re: AMBER: What's the meaning of NTYPES?

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Wed Jun 21 2006 - 15:59:23 CDT

Hi Thomas,

Thanks for the response! No, I'm not saying that. What you said is 'NATYP'
in the topology file. In the manual, its explanation is "number of atom
types in parameter file". But in topology file, there's another varible
"NTYPES", it's not the same as "NATYP". For example, in my complex system,
"NTYPES" is 11, it contains 36 atom types.
=====
   1 N N* N2 N3 NA NB NC
   2 H HS
   3 CT
   4 H1 H2 H4 H5 HA HC HP
   5 C C* CA CB CC CK CM CN CQ CR CW
   6 O O2
   7 OH
   8 HO
   9 S SH
  10 OS
  11 P
=====

Do you have a idea?

Thanks!

On Wed, 21 Jun 2006 18:55:06 -0300, Thomas Steinbrecher
<steinbrt_at_scripps.edu> wrote:

> Hi JunJun,
>
>> What's the meaning of NTYPES in topology file? I checked the manual, it
>> says NTYPES is the "total number of distinct atom types". What does the
>> "distinct" atom types mean? Does it mean some atom types are equal?
>
> Thats true, only a handful of atom types are used to describe a typical
> Md-system, e.g. all hydrogen atoms attached to water molecules are of
> type 'ho' and thus equal in charge and vdW radius..
>
> Regards,
>
> Thomas 

-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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