[gmx-users] pdb2gmx atom not found

[Una Bjarnadottir]

> 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
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