AMBER Archive (2006)

Subject: Re: AMBER: problem with saving the parameters file

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jul 05 2006 - 13:23:05 CDT

> I have solvated the protein using TIP3PBOX 8 2. When I try to save the topology and coordinates file ( .top and .rec) using the following command
>
> >saveamberparm prot rec.top rec.crd
>
> the files are not being saved with the following error message.
>
> could not find angle parameter: N-CT-N
> could not find angle parameter: N-CT-N
> could not find angle parameter: N-CT-N
> could not find angle parameter: N-CT-N
> building proper torsion parmeters
>
> 1-4: ang 5-9 duplicates bond ('triangular' bond) or angle ('square' bond)
> 1-4: ang 2-7 duplicates bond ('triangular' bond) or angle ('square' bond)
> building imroper torsion parameters
> total 708 improper torsions applied
> building H bond parameters
> parameter file was not saved.
>
> Can anyone help me to properly save the .top and .rec with out these messages.
 
You might want to try saving the unsolvated system first, and
if you have added your own ligand you might want to check it
for correctness of atom types (missing angle params) and
topology (triangular/square bonds). Or possibly there
are unusual crosslinks within your protein?

Bill
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