[gmx-users] pdb2gmx fatal error

[Justin Lemkul]

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.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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