[gmx-users] Understanding comments in pdb2gmx output

[Johnny Lu]

Does the pdb file have alternative conformations for some side chains or
atoms?

Like a side chain may have 50% chance to be rotated left, and 50% chance to
be rotated right.
The crystallographer recognized these two possibilities, and give each
possibility a 0.5 occupancy.

It may look like

LYSA
LYSB

with A for one conformation, and B for another conformation.

On Fri, Oct 17, 2014 at 6:08 PM, Agnivo Gosai <agnivogromacs14 at gmail.com>
wrote:

> Dear Gromacs Users
>
> I am working with a complex of Human Thrombin - DNA aptamer ( pdb id 1HAO )
> . I am using GROMACS 4.5.7 having the force field AMBER99SB-ParmBSC0 ported
> into it. I had cleaned the PDB file off crystal waters and a small chemical
> ligand ( which I dont require ) before passing it through pdb2gmx.
>
> The topology has been successfully generated.
>
> However I am concerned with the following comments in the output of pdb2gmx
> , I am copy pasting 3 blocks from the output :-
>
> #############################
> There are 3 chains and 0 blocks of water and 247 residues with 2590 atoms
>
>   chain  #res #atoms
>   1 'D'    15    315
>   2 'L'    27    222
>   3 'H'   253   2053
>
> WARNING: there were 0 atoms with zero occupancy and 9 atoms with
>          occupancy unequal to one (out of 2590 atoms). Check your pdb file.
> #################################
> Processing chain 3 'H' (2053 atoms, 253 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
>  protonation. 395 donors and 366 acceptors were found.
> There are 535 hydrogen bonds
> Will use HISE for residue 57
> Will use HISE for residue 71
> Will use HISE for residue 91
> Will use HISE for residue 119
> Will use HISE for residue 230
> Now there are 253 residues with 4078 atoms
> ############################################
> Chain time...
> Making bonds...
> Warning: Long Bond (2429-2431 = 0.805851 nm)
> Number of bonds was 4137, now 4136
> ##########################3
>
> I would like to know the meaning of these messages. Also I am reading the
> GROMACS manual for further info.
>
> Best ,
>
> Agnivo
> Iowa State , USA
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