[gmx-users] dna-protein simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Sep 19 15:37:07 CEST 2008

Hi Prasun,

Indeed, there's more to the conversion of DNA for gromacs input.
Some sed lines:

sed -e '{/^.\{13\}H.\'/d; /^.\{13\}H7. THY/d; /^.\{12\}H5''/d}'

should get you rid of these hydrogens, and

sed -e '{s/\(^.\{13\}C\)7  THY/\15M THY/}'

should set the proper name for the DTHY methyl group.

As I've mentioned, these lines come from a script I wrote. I just
copy-pasted the sed portions, but I'm not sure that they work out of
the box. I'll see if I can make the script independent of Haddock
parameter files and make it available. It does use CNS though...



On Fri, Sep 19, 2008 at 3:26 PM, prasun kumar <prasun30 at gmail.com> wrote:
> Hello Tsjerk
> I have solved that problem, now while running PDB2GMX command its giving
> following error
> C7 was not found in rtp file
> so I just compared the atom type in rtp file for DTHY and corresponding pdb
> file and replace C7 by C5M.
> i used -ignh option also,still I am getting warning like
> H1 is not found
> H3 is not found
> but the program is running its giving error while running GROMPP step.
> can you please help me in removing this error
> with regards
> --
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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