[gmx-users] Understanding comments in pdb2gmx output

[Justin Lemkul]

On 10/18/14 3:59 PM, Agnivo Gosai 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.
>
> 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.

Yes.  The output indicates that atoms 2429 and 2431 are separated by 0.805851 
nm.  The warning is triggered when the atoms are bonded, so this indicates 
something very bizarre is still happening.

> 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 ) ?
>

Unlikely.

> 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 ?

It's a generic warning.  Gromacs tools do not care about CONECT records; bonds 
are generated by pdb2gmx from .rtp entries, which are known residues.  Other 
Gromacs tools ignore CONECT records, because the topology generated by pdb2gmx 
is definitive for what the bonded structure is.  Everything else is irrelevant.

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

The number of residues has not increased.  The number of atoms increases because 
hydrogen atoms that were not present in the crystal structure have been added.

-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

==================================================