[gmx-users] Re: DNA in gromacs

[Anton Feenstra]

mymonii at pob.huji.ac.il wrote:
> I found your answer in gromacs user list.
> 
> It  will be very helpful, if you could send me *pdb and  *itp files with DNA
> So I could to see the format of those files and maybe finally
> To understand what is wrong in my files.

I'm sorry, but I'm not sure to which of my answers you are referring.
I have not worked with DNA myself, and although I am now starting a
cooperation with someone who does, I still have no experience with it.

I do know that it can be a bit tricky to get pdb2gmx to accept your DNA
pdb files. Especially residue and atom names have to correspond to those
in the .rtp entries. For hydrogens this is extra tricky, since these can
be generated when they are missing, and are assigned names automatically.
I assume you did not use the -ignh option of pdb2gmx?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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