[gmx-users] building a peptide

[Erik Lindahl]

David wrote:

>On Tue, 2002-07-09 at 21:53, storme at rpi.edu wrote:
>
>>Hi,
>>	I am trying to build an eight alanine residue peptide capped at
>>either end with ACE and NAC. However, when I use pdb2gmx it gives me the
>>following error:
>>
>>Fatal error: atom N not found in residue 1ACE while combining tdb and rtp
>>
>>The error doesn't make a whole lot of sense since there is atom N in ACE.
>>If you have any ideas any help would be great. Thanks alot
>>		
>>
>There is ACE (CH3-CO) and NAC (NH2-CH3-CO) (I think). Check ffgmx.rtp
>			
>
Hi,


You will probably need to:

1. Have at least the heavy atoms of the capping residue in your PDB file
2. Use the '-ter' option to pdb2gmx and select 'no terminus' since you 
already have capping residues.

Cheers,

Erik


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