[gmx-users] .top file after using amber2gromacs

[Chetan Mahajan]

Hi All,

I would like to add to following question that simulation has so far been
physically ok. Thus, mostly having those zeroes there may not have
mattered, since later sections in the same .top file have masses and
charges specified.

Thanks
Chetan


On Sun, Mar 2, 2014 at 10:24 PM, Chetan Mahajan <chetanvm10 at gmail.com>wrote:

> Hi All
>
> I have gromacs files generated using acpype tool acting on Amber files
> originally.
> I need to know the meaning of certain terms in that *.top file (email with
> attachment of .top file got blocked due to attachment). Unfortunately, I
> can't find on the web, any material regarding that. It would be great, if
> anyone could comment on the following.
>
> *1. What is the meaning of terms under defaults option at the top of the
> file (pasted below)?*
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ   fudgeQQ
>      1                    2                 yes                  0.5
>  0.8333
>
> * 2a. ** Is atomtypes section needed? (sample .top file on gromacs
> website does not have it) (pasted after 2b question)**In this atomtypes
> section, the Amber2gromacs tool keeps mass and charge of each atom as zero.
> Would a simulation with these places zero be a valid simulation **?* My
> guess is yes. THis is since, corresponding values are available later in
> atoms section. The purpose of asking this question is that I have to be
> sure of the runs I have made, that nothing has gone wrong in having those
> zeros.
>
> * 2b.I see several enigmatic terms such as bond type p type, Amb. Can you
> explain these terms, if they are necessary at all? Why last two columns for
> Amb?*
>
> (part of the data for both 2a and 2b pasted below)
> [ atomtypes ]
> ;name   bond_type     mass     charge   ptype   sigma         epsilon
>   Amb
>      Ti       Ti              0.00000  0.00000   A     1.39461e-01
> 6.08772e-02 ; 0.78  0.0145
>     OT       OT           0.00000  0.00000   A     2.87832e-01
> 8.29687e-02 ; 1.62  0.0198
>     HW       HW          0.00000  0.00000   A     0.00000e+00
> 0.00000e+00 ; 0.00  0.0000
>
> *4.WHat is cgnr? how is it different from nr? (it appears in atoms
> section, example below)*
>
>  nr  type  resi  res  atom  cgnr     charge      mass       ; qtot
> bond_type
>      1   Ti     1   iO2    TI    1     1.691002     47.86700 ; qtot 1.691
>
> Thanks
>