»Ø¸´£º Re: »Ø¸´£º Re: »Ø¸´£º Re: »Ø¸´£º Re: [gmx-users] about using amb2gmx.pl

Justin A. Lemkul jalemkul at vt.edu
Sun Feb 17 13:52:53 CET 2008

Search for John Kerrigan's enzyme-ligand tutorial.  It explains in clear detail
everything you will need to do.  Ignore the part about using PRODRG for your
chromophore, as you apparently already have this information from antechamber.

For the future, it would be more clear to post this type of information:

1. What structures (pdb/gro, doesn't really matter) you already have
2. What topologies you have, and how you generated them
3. Specific errors you are having (from pdb2gmx, etc), not simply "I cannot get
top and gro for the whole complex."  It leaves us wondering what you have or
haven't tried doing.


Quoting xi zhao <zhaoxiitc2002 at yahoo.com.cn>:

> Dear sir:
>   Is my english weak? I want to simulate pdb:1O5P (www.rcsb.org), I use amber
> force field parms in the gromacs. Under this condition, pdb2gmx can not
> produce chromophore top in the pdb,so I use antechamber and amb2gmx.pl to
> produce chromophore gro and top files accoding to ffamber website. I do not
> know how to produce gro and top of entire system.
> Mark Abraham <Mark.Abraham at anu.edu.au> дµÀ£º
>   xi zhao wrote:
> > Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding
> > gro top files, but I can only produce chromophore gro and top file using
> > amb2gmx.pl .Are you clear ?
> No. If you have a structure file already, then you need to read what I
> wrote earlier. If you don't have a structure file already, then you need
> to read what I wrote earlier. If you have some problem getting an
> existing AMBER structure+prmtop to convert properly, then you haven't
> communicated that. If you haven't got an AMBER structure+prmtop, then
> give up on amb2gmx.pl
> Try explaining your problem in English to a friend who doesn't fully
> understand the science. Then apply the lessons you learned there to
> describing the problem here :-)
> Mark
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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