[gmx-users] Can I use the pdb2gmx to produce the .top file of dendrimers?

David van der Spoel spoel at xray.bmc.uu.se
Mon Jun 21 14:30:55 CEST 2004

On Mon, 2004-06-21 at 13:09, Hanming wrote:
> Hi, all, 
> In some polymers like dendrimers such as Poly(amide amine) or 
> poly(propyleneimine) there are repeated units in it. But the repeated unit
> has more than one connetted point to the following repeated units. That is,
> it is not a linear molecule. Can I define the repeated units as a residue
> and use pdb2gmx to produce my .top file.If it works how? 
In principle yes, but it depends on how regular the polymers are.
pdb2gmx is usually for linear polymers, but it can also make connections
through sidechains (e.g. cys-cys) which are defined specially. If your
molecule is rather simple you could also try the x2top utility. 

All possibilities will require hacking some files:
pdb2gmx: XXX.rtp XXX.hdb specbond.dat xlateat.dat
x2top:   XXX.n2t
> Thanks, 
> Ming 
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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