AMBER Archive (2006)

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

From: Wei Zhang (zweig_at_scripps.edu)
Date: Thu Jun 22 2006 - 11:18:38 CDT

NTYPES is 11 becauses some atoms types have same VDW parameters. when
generate
prmtop, leap will check the VDW parameter of each type, and compress the
types with
same VDW parameter into one type. That is why you have 36 atom type but
only 11
for NTYPES.

Sincerely,

Wei

JunJun Liu wrote:

> 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
>
>
>
>

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