[gmx-users] question on Cholesterol topology file

[Erik Lindahl]

On Oct 19, 2005, at 3:25 PM, Jim (Rui) Qiao wrote:

> Dear Gromacs users:
>
> I am trying to use the Cholesterol topology file uploaded by Monika  
> Hoeltje on the Gromacs server, and have a few questions:
>
> In the "cholesterol.itp" file, it writes:
>
> [ atoms ]
> ;   nr    type   resnr  residu    atom    cgnr    charge   ; total  
> charge
>      1     CH3       1    CHOL     C1        1     0
>      2      CB       1    CHOL     C2        2     0
> ...
> ...
> [ bonds ]
> ;  ai    aj funct           c0           c1
>     1     2     1        0.153         334720.
>     2     3     1        0.153         334720.
>     3     4     1
>     4     5     1
>     5     6     1
> ....
> ....
>
> It is noticed that the some parameters under [bonds] are not given.  
> What does this mean? How will gromacs know where to look for these  
> parameters?

If you don't specify any explicit parameters grompp will pick up the  
default ones for these atomtypes from the forcefield.

Normally you only specify explicit parameters to override the default  
values.

Cheers,

Erik


-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214




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