[gmx-users] pdb2gmx

‪farial tavakoli‬ ‪ farial.tavakoli at ymail.com
Thu Jul 20 14:06:58 CEST 2017

 I want to create a .gro and .top file from my protein that contains 379 aminoacids in it's .pdb file by using gromos96 54a7 force field:
pdb2gmx -f protein.pdb -o protein.gro -water spce -ignh
but when gro and topology files are created , I see that message:
Start terminus GLY-12: GLY-NH3+
End terminus PRO-379: COO-
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 368 residues with 3856 atoms
Making bonds...
Number of bonds was 3938, now 3933
Generating angles, dihedrals and pairs...
Before cleaning: 6090 pairs
Before cleaning: 8285 dihedrals
Making cmap torsions...There are 2746 dihedrals, 2028 impropers, 5756 angles
          6090 pairs,     3933 bonds and     0 virtual sites
Total mass 42175.307 a.m.u.
Total charge -0.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.46#

Writing coordinate file...

Back Off! I just backed up HDAC2.gro to ./#HDAC2.gro.1#
        --------- PLEASE NOTE ------------
You have successfully generated a topology from: HDAC2.pdb.
The Gromos54a7 force field and the spce water model are used.
        --------- ETON ESAELP ------------

However, i ignored this message and continued to use grompp
gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

but faced to this message:
  gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.29#
Setting the LD random seed to -1863558486
Generated 168 of the 1653 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   368    Protein residues
There are: 11240      Water residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 79005.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 72x72x72, spacing 0.114 0.114 0.114
Estimate for the relative computational load of the PME mesh part: 0.10
This run will generate roughly 3 Mb of data

Back Off! I just backed up ions.tpr to ./#ions.tpr.36#

Is there anyone to help me? Why pdb2gmx didnt consider all 379 amino acids of my protein and why GOMACS excluded 3 bonded neighours of the protein and SOL?and would you please tell what ' removing all charge groups because cutoff-scheme=Verlet ' means ? I t means the system is neutral ?

thanks in advanceFarial

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