[gmx-users] Understanding comments in pdb2gmx output

[Justin Lemkul]

On 10/17/14 6:08 PM, Agnivo Gosai 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.

Some crystal structures have multiple conformations for some residues.  This 
note tells you to verify that this may be the case here and you should verify 
the contents of the input file are giving you what you want.

> #################################
> 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

pdb2gmx guesses histidine protonation states based on H-bonding networks unless 
you tell it what protonation states to assign.  If you have information based 
on, e.g. pKa calculations, you should verify that what pdb2gmx detects is what 
is correct.

> ############################################
> Chain time...
> Making bonds...
> Warning: Long Bond (2429-2431 = 0.805851 nm)
> Number of bonds was 4137, now 4136
> ##########################3

This suggests you have missing atoms or a very bad geometry.  This could be 
related to the first message about occupancies.  Likely there is something funky 
in the coordinates, but given that pdb2gmx has told you what the weird atoms 
are, you can easily check both input and output.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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