[gmx-users] bad bond in polymer

[Justin A. Lemkul]

nicegromacs wrote:
> 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
> 
> -------------------------------------------------------
> 

It looks like pdb2gmx is finding some kind of undefined residue.  Can you post 
the .pdb file?

-Justin

> "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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> 

-- 
========================================

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

========================================