[gmx-users] nucleic acid PDB input files

[Cameron Mura]

Hi Andrey,

Thanks for the tip -- I was directed to a similar post by Graham Smith 
regarding ff*.hdb files 
(http://www.gromacs.org/pipermail/gmx-users/2002-November/003394.html).
I finally was able to get pdb2gmx to work (without using the -missing 
option) by modifying the residue topology file for the G43a1 FF and the 
corresponding *.hdb file.  I ended-up adding a 5' nucleotide without 
phosphate (not re-parameterized, but that's OK b/c not running MD or 
anything like that with it... just building a solvated structure).

Thanks again,
Cameron


=== Andrey V. Golovin wrote (on 03/01/2005 05:02 AM): ===

>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
>----------------------------------------------------------------
>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
>-----------------------------------------------------------------
>
>
>---------- 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 -------
>
>
>  
>