[gmx-users] nucleic acid PDB input files

[Andrey V. Golovin]

Hi
First what ff are you using ?
Second you have to check your ff???.hdb file in $GROMACS/share/top probably
all records for  nucleic acids are missing there.



----
Best regards, Andrey
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Andrey V. Golovin
Ph.D,Professor assistant    tel: +7 (095) 939-5305  
Bioengineering and
Bioinformatics Department              
Moscow State University     fax: +7 (095) 939-3181
119899 Moscow            E-mail: golovin at genebee.msu.su
Russia                      web: http://rnp-group.genebee.msu.su
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---------- Original Message -----------
From: Cameron Mura <cmura at ucsd.edu>
To: gmx-users at gromacs.org
Sent: Mon, 28 Feb 2005 13:20:33 -0800
Subject: [gmx-users] nucleic acid PDB input files

> Hi,ff???.hdb
> Would anyone who's successfully used "pdb2gmx" to convert a DNA or 
> RNA starting structure in PDB format to Gromacs format please send 
> me a sample of their input PDB file?? I'd greatly appreciate it, as 
> I can't seem to get beyond errors of this sort when running pdb2gmx:
> 
> > ...
> > ...
> > Making bonds...
> >
> > WARNING: atom H21 is missing in residue DGUA 1 in the pdb file
> >          You might need to add atom H21 to the hydrogen database of 
> > residue DGUA
> >          in the file ff???.hdb (see the manual)
> >
> > WARNING: atom H22 is missing in residue DGUA 1 in the pdb file
> >          You might need to add atom H22 to the hydrogen database of 
> > residue DGUA
> >          in the file ff???.hdb (see the manual)
> >
> > WARNING: atom H1 is missing in residue DGUA 1 in the pdb file
> >          You might need to add atom H1 to the hydrogen database of 
> > residue DGUA
> >          in the file ff???.hdb (see the manual)
> >
> > Fatal error: There were 3 missing atoms in molecule Protein, if you 
> > want to use this incomplete topology anyhow, use the option -missing
> 
> Thanks,
> Cameron
> 
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------- End of Original Message -------