[gmx-users] pdb2gmx atom not found

[Alan Dodd]

I'd suggest that you check your column widths -
perhaps the M is being truncated off the front.  It
can happen quite frequently with non-standard entries,
particularly.

--- Una Bjarnadottir <una.bjarnadottir at ucd.ie> wrote:

> > Una Bjarnadottir wrote:
> > 
> >>Dear users,
> >>
> >>I keep getting this error when starting runs;
> >>
> >>Opening library file aminoacids.dat
>
>>-------------------------------------------------------
> >>Program pdb2gmx, VERSION 3.3
> >>Source code file: add_par.c, line: 221
> >>
> >>Fatal error:
> >>Atom NZ1 not found in rtp database in residue
> LYSH, it looks a bit like NZ
>
>>-------------------------------------------------------
> >>
> >>There is no Atom NZ1 in the .rtp file or the pdb
> file I'm using. No .top 
> >>file is generated so no run.
> >>
> >>I would really appreaciate any comments on how to
> fix this.
> > 
> > rename the atom in the pdb file
> 
> Yeah but the strange thing is there is no NZ1 in my
> pdb file or other 
> files.  I only find MNZ1 in atommass.dat and
> vdwradii.dat files.
> 
> Cheers, Una
> > begin:vcard
> fn:Una Bjarnadottir
> n:Bjarnadottir;Una
> org:UCD;UCD School of Biomolecular and Biomedical
> Science  
> adr:Belfield;;Conway Institute;Dublin;;4;Ireland
> email;internet:una.bjarnadottir at ucd.ie
> tel;work:+353 (1) 716 6874 
> version:2.1
> end:vcard
> 
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