[gmx-users] RNA ffgmx.hdb problems

[Florian Haberl]

Hi,

On Thursday, 14. June 2007 13:43, dwunnick at uni-osnabrueck.de wrote:
> Hello all,
>
> as a beginner I try gromacs for the first time. At first my aim is just
> the energy minimization of a small RNA aptamer. I started to convert my
> pdb file into a gromacs structure file with pdb2gmx and failed. I obtained
> this error:
>
> Fatal error: Atom H1* in residue GUA 2 not found in rtp entry with 27
> atoms while sorting atoms. Maybe different protonation state. Remove this
> hydrogen or choose a different protonation state. Option -ignh will ignore
> all hydrogens in the input.
>
> So I try the -ignh and get another error and some warnings like:
>
> WARNING: atom H21 is missing in residue GUA 1 in the pdb file. You might
> need to add atom H21 to the hydrogen database of residue GUA in the file
> ff???.hdb (see the manual)
>
> Fatal error: There were 175 missing atoms in molecule Protein, if you want
> to use this incomplete topology anyhow, use the option -missing
>
> Cause I use the Gromacs force field which resorts to the file ffgmx.rtp
> and ffgmx.hdb, I check both files. All four nucleotides exist in the
> ffgmx.rtp but no one in the .hdb. So I add the following in-between the
> alphabetical order as suggested in old mails/questions:

for simulations with RNA or DNA use 

http://folding.stanford.edu/ffamber/

Gromos force field won`t give you good datas for RNA or DNA.

>
> ADE     3
> 1       2      H2*       O2*       C2*       C3*
> 2       3      H61       N6        C6        N1
> 2       3      H62       N6        C6        N1
> GUA     4
> 1       2      H2*       O2*       C2*       C3*
> 2       3      H21       N2        C2        N1
> 2       3      H22       N2        C2        N1
> 1       1      H1        N1        C6        C2
> CYT     3
> 1       2      H2*       O2*       C2*       C3*
> 2       3      H41       N4        C4        N3
> 2       3      H42       N4        C4        N3
> URA     2
> 1       2      H2*       O2*       C2*       C3*
> 1       1      H3        N3        C2        C4
>
> Afterwards I change the number of aminoacids.dat to 53 and add the
> abbreviations. Then I try the command "pdb2gmx -ignh -f Aptamer.pdb" again
> and obtained the same error - 175 missing atoms! And all missed atoms are
> exactly the atoms I add to the .hdb file.
> So, I did something wrong and I have to say, I have no idea what. I
> apogolize about this really long Mail. I hope somebody can help me out of
> this.
>
> With best and hopefully regards,
>
> Dorith Wunnicke
>
>
>
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Greetings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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