[gmx-users] N-terminal PGLU and C-term amidation

Henry Hocking H.G.Hocking at uu.nl
Tue Oct 18 16:13:01 CEST 2011


I am new to gromacs. I am applying the pdb2gmx tool to a peptide that  
has an N-term pyroglutamate and a C-term amidation. The OPLS  
forcefield has an entry for PGLU.

I used the -ter flag of pdb2gmx to define protonation states of the  
termini. While this works fine for the C-term (choosing 3:None) I run  
into trouble with the PGLU at the N-term.

In my input pdb the nitrogen of PGLU is attached to CA, CD and one  

However when prompted 'Select start terminus type for PGLU-1' there is  
no NH option. If I select 'None' I get "Fatal error: There is a  
dangling bond at at least one of the terminal ends." If I chose NH2 I  
end up with too many protons at my N-terminus.

If I leave out the -ter flag altogether I get problems with my C- 
terminus: "Fatal error: atom C not found in building block 23NH2 while  
combining tdb and rtp".

How would I solve this?



Henry Hocking, PhD

Utrecht University
Bijvoet Center for Biomolecular Research
Padualaan 8
3584 CH Utrecht, The Netherlands

Phone: +31-30-2532875
Fax: +31-30-253 7623
E-mail: H.G.Hocking at uu.nl

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111018/4fbd88aa/attachment.html>

More information about the gromacs.org_gmx-users mailing list