[gmx-users] Understanding comments in pdb2gmx output

[Agnivo Gosai]

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.

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