[gmx-users] pdb2gmx fatal error

[Ali Khodayari]

Dear Justin,

Thank you for your full explanation. That made it all clear now.

Kind regards,
Ali

> On 13 Nov 2018, at 00:57, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 11/8/18 1:37 PM, Ali Khodayari wrote:
>> Dear Justin,
>> 
>> Thank you for your response. Yet, I have not been able to solve the problem.
>> 
>> The structure looks fine but gromacs is complaining about a dangling atom at
>> one of the terminal ends, if I choose no terminal to be added. While,
> 
> You can't "see" a dangling bond by visualizing the structure. That term refers exclusively to an incomplete terminus in terms of the *topology* that is being generated for the system. Maybe atoms are missing or an inappropriate terminal patch is being applied; either would generate that error. But again I emphasize the fact that a chain of glucose has first and last residues that are structurally and topologically different from internal, linked monomers. It's basic chemistry.
> 
> <snip>
> 
>> ATOM     27  O3  GLC0    2      3.909   5.661   5.002  1.00  0.04
>> O
>> ATOM     28  HO4 GLC0    2      4.850   3.729  10.263  1.00  0.00
>> H
>> ATOM     29  O1  GLC0    1      3.396   2.685   4.467  1.00  0.04
>> O
> 
> Here's your problem - your residue numbers alternate back and forth between 1 and 2. pdb2gmx ignores these and uses its own numbering, incrementing the internal counter whenever the residue number changes. So to pdb2gmx, your input file is full of incomplete residues.
> 
>> ATOM     30  O5  GLC0    2      4.225   2.770   8.173  1.00  0.04
>> O
>> ATOM     31  O6  GLC0    2      3.558   0.309   5.328  1.00  0.04
>> O
>> ATOM     32  H1  GLC0    2      2.572   4.115   8.609  1.00  0.00
>> H
>> ATOM     33  H2  GLC0    2      5.244   5.151   7.307  1.00  0.00
>> H
>> ATOM     34  H3  GLC0    2      2.361   4.651   6.153  1.00  0.00
>> H
>> ATOM     35  H4  GLC0    2      5.141   3.258   5.636  1.00  0.00
>> H
>> ATOM     36  H5  GLC0    2      2.480   2.262   6.979  1.00  0.00
>> H
>> ATOM     37  H61 GLC0    2      3.879   0.196   7.468  1.00  0.00
>> H
>> ATOM     38  H62 GLC0    2      5.286   0.920   6.494  1.00  0.00
>> H
>> ATOM     39  HO2 GLC0    2      2.496   6.480   7.836  1.00  0.00
>> H
>> ATOM     40  HO3 GLC0    2      5.015   5.674   4.919  1.00  0.00
>> H
>> ATOM     41  HO6 GLC0    2      2.453   0.270   5.418  1.00  0.00
>> H
>> ATOM     42  O3  GLC0    1      3.852   1.653  -0.348  1.00  0.00
>> O
> 
> As above, now you're again going back and forth between 1 and 2, so pdb2gmx sees a new residue, which is not correct.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> 
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
> 
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