[gmx-users] Re: How to obtain the .gro and .top files for dendrimers

[Mark Abraham]

wuxiao wrote:
> Dear gmx users,
>   In order to get more direct help, some words need to be added to the 
> question for the first time.

That's a good idea.

>   The dendrimer I want to study is just PAMAM, ethylenediamine (EDA) 
> cored and amine surface poly(amidoamine). The pdb file for the PAMAM has 
> assumed to be obtained, and I want to generate the .gro and .top files 
> from the pdb file using pdb2gmx. 

You don't need a .gro file. It's a by-product of pdb2gmx, however.

> According to the advice, some files 
> need to be modified to make it implement successfully. so my question 
> becomes: How to modify those files? Thanks a lot.

As I said last time, you'll need to read and understand chapter 5 in
detail. You need .rtp file entries for all of your monomeric units and
half-capped monomeric units. This will require picking a MM forcefield,
looking at how the existing .rtp file entries work for it, and adapting
that knowledge to your own needs. You will also need to understand the
specbond.dat mechanism to facilitate branching. This is probably not
well-travelled territory, so you will have to do a lot of work. Doing
some protein-specific GROMACS tutorials is also wise - particularly ones
that use disulfide links, since that will teach you about specbond.dat.

In general, you stand a better chance of getting useful answers to
focussed questions that show you've tried to get your own information
and solve your own problems. "How to modify these files" sounds like you
want someone to do it all for you :-)

Mark