[gmx-users] pdb2gmx

[David van der Spoel]

On Tue, 2003-11-11 at 22:25, Luciano Tavares wrote:
>  Hi gmx's,
> 
>  I was trying to convert a peptide structure in *.pdb to *.gro using
> pdb2gmx and it showed:
> 
> 
> Using ffoplsaa force field
> Opening library file /usr/local/gromacs/share/top/ffoplsaa.atp
> Atomtype 696
> Reading residue database... (ffoplsaa)
> Opening library file /usr/local/gromacs/share/top/ffoplsaa.rtp
> Residue 50
> Sorting it all out...
> Opening library file /usr/local/gromacs/share/top/ffoplsaa.hdb
> Opening library file /usr/local/gromacs/share/top/ffoplsaa-n.tdb
> Opening library file /usr/local/gromacs/share/top/ffoplsaa-c.tdb
> Processing chain 1 (1623 atoms, 160 residues)
> Opening library file /usr/local/gromacs/share/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> There are 240 donors and 241 acceptors
> There are 1211 hydrogen bonds
> Fatal error: Atom H in residue PRO 1 not found in rtp database
>              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.
> 
> 
> What is the better option?  My structure was generated by Sybyl. Before, I
> had choose the option -ignh, but I have been problem with EM.
> 
> Thanks in advance...

apart from -ignh you might want to try -ter
and manually selected the right N-terminus

> 
> Luciano
> 
> 
> ######################################################################
> ##      Luciano Tavares da Costa * ltcosta at universiabrasil.net      ##
> ##           Laboratory of Theoretical Chemistry-DQ UFSCar          ##
> ##             Caixa Postal 676      | PO Box 676                   ##
> ##       13565-905 Sao Carlos - SP   | 13565-905 Sao Carlos - SP    ##
> ##                          Brasil   | Brazil                       ##
> ######################################################################
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++