[gmx-users] pdb2gmx atom not found

Una Bjarnadottir una.bjarnadottir at ucd.ie
Thu Mar 9 19:17:45 CET 2006

> 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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: una.bjarnadottir.vcf
Type: text/x-vcard
Size: 250 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060309/e4c40a9b/attachment.vcf>

More information about the gromacs.org_gmx-users mailing list