[gmx-users] Problem simulating DNA

[Maik Goette]

Hi

We need more infos to help you.
At first: Which forcefield are you using?
At second: Did you modify your PDB entries of the residue and atom names 
to be understood by the forcefield/pdb2gmx?

For I am quite sure, you are not using the amber ff-port, you should.
Search the mailing list for that (done by Eric Sorin).
Then, you have to modify your PDB according to the FF.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Manish Datt wrote:
> hi all
> 
> i`m new to gromacs and am tyring to simulate a dna molecule. but i am
> facing following problem on running pdb2gmx
> 
> ********A PORTION OF OUTPUT********
> 
> WARNING: atom H41 is missing in residue DCYT 47 in the pdb file
>          You might need to add atom H41 to the hydrogen database of
> residue DCYT
>          in the file ff???.hdb (see the manual)
> 
> 
> WARNING: atom H42 is missing in residue DCYT 47 in the pdb file
>          You might need to add atom H42 to the hydrogen database of
> residue DCYT
>          in the file ff???.hdb (see the manual)
> 
> 
> WARNING: atom H41 is missing in residue DCYT 48 in the pdb file
>          You might need to add atom H41 to the hydrogen database of
> residue DCYT
>          in the file ff???.hdb (see the manual)
> 
> 
> WARNING: atom H42 is missing in residue DCYT 48 in the pdb file
>          You might need to add atom H42 to the hydrogen database of
> residue DCYT
>          in the file ff???.hdb (see the manual)
> 
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3
> Source code file: pdb2top.c, line: 697
> 
> Fatal error:
> There were 102 missing atoms in molecule Protein, if you want to use this
> incomplete topology anyhow, use the option -missing
> -------------------------------------------------------
> 
> kindly help me solve this problem
> 
> regards,
> 
> Manish Datt
> Research Scholar
> Bioinformatics Centre
> Institute of Microbial Technology
> Sector 39A, Chandigarh-160036
> India.
> 
> 
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