[gmx-users] Understanding comments in pdb2gmx output

[Mark Abraham]

On Sat, Oct 18, 2014 at 9:59 PM, Agnivo Gosai <agnivogromacs14 at gmail.com>
wrote:

> Dear Users
>
> Thrombin-Aptamer complex : PDB ID 1HAO
>
> Thanks for the earlier comments. I appreciate the efforts of all users and
> developers for taking their time out and helping.
>
> I checked the pdb file for the "occupancies" not equal to 1.000 and found 9
> atoms having 0.001 ocuupancy. So, I manually changed the values to 1.000.
>

You should understand and resolve the reason for the warning, not just
suppress the symptoms. That means reading the PDB file to find out why the
occupancies are not one. I expect you will find that the long bond and
these residues are related.

Mark

As , Mr. Lu and Dr. Lemkul said I checked for multiple conformations in the
> protein part but found out that 0.001 occupancy was assigned to 9 atoms in
> the 15-mer oligonucleotide (aptamer) part.
>  The residue names were DT.
>
> After this , I again passed the curated pdb through pdb2gmx and cam across
> the following warning :-
> #######################################################################
> Generating any missing hydrogen atoms and/or adding termini.
> 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
> #########################################################################
>
> Now Dr. Lemkul earlier said that there can be missing atoms or a very bad
> geometry. I also thought it could be regarding the earlier warning on
> occupancies. However this "long bond" warning is still showing up. Does
> anyone have any idea as to how to fix this ? Is it possible to do it
> manually ? In the expression 2429 - 2431 = 0.805851 nm are the 1st two nos.
> atom nos ??
> Am I facing this issue because I manually deleted one ligand (inhibitor)
> bound to the active site of the thrombin protein and also manually removed
> all lines containing HOH ( crystallized water ) ?
>
> I checked the GROMACS online help and it talks about missing atoms , there
> is no missing atom warning in pdb2gmx output !!
> <<<<<<<<<<<<<<<<<
> I am copy pasting two other blocks , as I am unable to understand their
> meaning :-
>
>
> #############################################################################
> WARNING: all CONECT records are ignored
> Read 'DNA 5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'; ;
> ALPHA-THROMBIN LIGHT CHAIN; ALPHA-THROMBIN HEAVY CHAIN', 2590 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> 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
> All occupancies are one
>
> *What is the meaning of this warning ???* In the web , I found a post
> saying for proteins it is ok , but I also have DNA in my system. Any
> suggestions ?
>
> #############################################################################
> Writing topology
> Including chain 1 in system: 488 atoms 15 residues
> Including chain 2 in system: 449 atoms 27 residues
> Including chain 3 in system: 4078 atoms 253 residues
> Now there are 5015 atoms and 295 residues
> Total mass in system 37060.423 a.m.u.
> Total charge in system -11.000 e
>
> *Now , the number of residues have increased and the total no. of atoms
> have also increased.* *I have also observed the same thing while completing
> Dr. Lemkul's tutorials. Why does this happen ? I have searched the web but
> could not find any satisfactory answer.*
>
> Thanks & Reagrds
> Agnivo Gosai
> Graduate Student
> Iowa State University
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