[gmx-users] pdb2gmx -ter

[Rainer Boeckmann]

you have to build these termini on your own and then choose "3: None"
best,
rainer

Raghunadha Reddy Burri wrote:

>Dear GMX users,
>
>I have a small question, 
>
>I have a peptide WITHOUT any N & C terminus but I want simulate with  N & C 
>terminus "ACE - peptide - NME" 
>
>When I using 
>
>pdb2gmx -f -ter -ignh
>
>3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>
>Select N-terminus type (start)
> 0: NH3+
> 1: ZWITTERION_NH3+
> 2: NH2
> 3: None
>
>What I can select now?
>
>means I was confused that asking for present peptide terminus (which have 
>None) or which I need .......
>
>Thank you for your time
>
>Looking for positive response 
>
>Burri
>
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>  
>

-- 
__________________________________________________________
Dr. Rainer Böckmann
Computational Structural Biology - Biochemistry Department
University of Zürich
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
tel:    ++41-(0)1-63-555-93 - fax:    ++41-(0)1-63-568-62
email: rainer at bioc.unizh.ch
http://www.biochem-caflisch.unizh.ch/rainer/
___________________________________________________________