[gmx-users] AEDANS & DDPM

[Jochen Hub]

jayant_jacques wrote:
>
>  
>  
> Hi all!
> I am attempting to simulate a protein with AEDANS and DABMI attached 
> to modified Cys. I got the .top files and .gro from PRODRG but on 
> attempting simulations I get the error
> Warning: 'DAB' not found in residue topology database,
>
Please keep in mind that the partial charges computed by prodrg should 
be applied with care. It may be a good idea to crosscheck your 
parameters by comparison to some experimental data.

Jochen

>
> So does any one have an idea how to build the residue topology for 
> AEDANS  or DABMI.  Is there any program out there that can help!!
> Thanks
> Jayant JAmes
>
> Jayasundar Jayant James
> Postdoc,
> Department of Veterinary and Comparative Anatomy, Pharmacology 
> and Physiology(VCAPP), Washington state university, Pullman 
> 99164-6520, USA.
> http://www.chick.com/reading/tracts/0001/0001_01.asp
> Phone office:335-5937, Cell:1-509-432-5790
>
> Magic Bricks 
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-- 
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************