[gmx-users] Need to confirm parameters.

[Sailesh Bataju]

>The easiest thing to do
>(solving this issue and #1) is to create an isobutane .rtp entry and have
>pdb2gmx do all the work for you.  It's very simple to do.

> -Justin

Thank you sir, I've exactly followed your steps. I've created
isobutane.rtp file and modified residuetypes.dat file by adding IBUT
as Protein and then created PDB file from prodrg server. Then using
pdb2gmx command finally got this result:

Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.r2b
Reading prodrg_ibut.pdb...
WARNING: all CONECT records are ignored
Read 14 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 1 residues with 14 atoms

  chain  #res #atoms
  1 ' '     1     14


WARNING: there were 4 atoms with zero occupancy and 8 atoms with
         occupancy unequal to one (out of 14 atoms). Check your pdb file.

Opening force field file /usr/share/gromacs/top/charmm36.ff/atomtypes.atp
Atomtype 412
Reading residue database... (charmm36)
Opening force field file /usr/share/gromacs/top/charmm36.ff/isobutane.rtp
Residue 1
Sorting it all out...
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.hdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.n.tdb
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.c.tdb
Processing chain 1 (14 atoms, 1 residues)
Identified residue IBUT0 as a starting terminus.
Identified residue IBUT0 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
No suitable end (N or 5') terminus found in database - assuming this residue
is already in a terminus-specific form and skipping terminus selection.
No suitable end (C or 3') terminus found in database - assuming this residue
is already in a terminus-specific form and skipping terminus selection.
Opening force field file /usr/share/gromacs/top/charmm36.ff/merged.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 14 atoms
Making bonds...
Warning: Short Bond (5-1 = 0.0259999 nm)
Warning: Long Bond (5-6 = 0.99084 nm)
Warning: Long Bond (1-2 = 0.944378 nm)
Warning: Long Bond (1-3 = 0.895661 nm)
Warning: Long Bond (1-4 = 0.866986 nm)
Warning: Long Bond (7-8 = 0.502204 nm)
Warning: Long Bond (7-9 = 0.567317 nm)
Warning: Long Bond (7-10 = 0.92202 nm)
Warning: Long Bond (11-12 = 0.592831 nm)
Warning: Long Bond (11-13 = 0.700231 nm)
Warning: Long Bond (11-14 = 0.729592 nm)
Number of bonds was 13, now 13
Generating angles, dihedrals and pairs...
Before cleaning: 27 pairs
Before cleaning: 27 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are   27 dihedrals,    0 impropers,   24 angles
            27 pairs,       13 bonds and     0 virtual sites
Total mass 58.124 a.m.u.
Total charge 0.000 e
Writing topology

Writing coordinate file...
		--------- PLEASE NOTE ------------
You have successfully generated a topology from: prodrg_ibut.pdb.
The Charmm36 force field is used.
		--------- ETON ESAELP ------------


1. According to the first warning like this "there were 4 atoms with
zero occupancy and 8 atoms with  occupancy unequal to one (out of 14
atoms)"

Is that a kind of error. Did I do any mistake as it said?

2. If i don't add IBUT as Protein in residuetypes.dat file I get error
like this however I get same topol.top file.

"Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 (14 atoms, 1 residues)
Warning: Starting residue IBUT0 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

-------------------------------------------------------
Program:     gmx pdb2gmx, version 2016.3
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 649)

Fatal error:
Residue 'IBUT' not found in residue topology database"

I've no idea whether I've successfully generated those files.

Thank you very much.