[gmx-users] bad bond in polymer

nicegromacs nicegromacs at live.cl
Fri Aug 14 17:40:07 CEST 2009

I follow some of the step of 
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I 
omitted the change in the .hdb file because I don't have explicit 
hydrogens). Well, I build a polymer with 3 units. The head (H), one repeat 
unit (R)and tail (T) for the polymer (H-R-T) and this gives ok, but when I 
add one more repetitive unit (H-R-R-T) I get the following error:
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Fatal error:
Atom CAM not found in residue 1083339441 while adding improper


"Stop Drinking My Beer !" (The Amps)

> nicegromacs wrote:
>>   CAG -CAM
> Defining a bond to a previous residue will certainly fail for at least one 
> terminus of your polymer chain.  You may find this post useful:
> http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
> If things still aren't working, please post the structure file, as well, 
> and identify the bond that is being formed that shouldn't.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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