[gmx-users] Pdb2gmx for cyclic Peptide

vidhya sankar scvsankar_agr at yahoo.com
Fri Sep 14 15:56:55 CEST 2012

Dear Justin Thanks Again for your reply 

                                              When I run  Pdb2gmx using -ter option for my Cyclic peptide and i have selected None for both termini as you instruct in the previous mail i have got error as follows

Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.

How to resolve these error
For you remembrance i have pasted the previous mail Discussion

I am doing MD  Cyclic Peptide  When I run  pdb2gmx , The Conect 
Infromation in pdb file are ignored . so that it is not able to connect 
the first and last residue in cycle .  But it construct and .top and.gro files  successfully while in .gro file the end residues are closed as 
NH3+ and COO-(charge)  (it means there is Bond between Nitrogen and 
carbon atom)
> It consider the N atom of first residue as 
NH3+    and   C atom as COO-(charge)   but I need to take N as peptide 
Nitrogen and C as Peptide carbon
> What Should i do  to invoke conect information when i run pdb2gmx tool

Use the -ter option and choose "None" for both termini.( Your Ansewr)

 Also Can i Directly Edit  (it means removing excess hydrogen and oxygen
 atom by ; symbol)   .top an .gro files and can i use  to proceed 
further ?

No.  This will cause errors in the [moleculetype] numbering and all successive   (Your Answer)
directives.  Re-run pdb2gmx instead.

Thanks in Advance 

With Regards

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