[gmx-users] Problem with pdb2gmx

[Justin Lemkul]

On 4/11/20 5:38 AM, Elham Taghikhani wrote:
>   Hi
> Thank you for your response.
> I added my ligand pdb file to the protein pdb file, then the ligand name as a protein/other (tried both) to the residuetype.dat file , but still it has warning in this case.
> As i said before I modified the rtp file too.This is the full screen of my terminal when I get the gro file by the gmx pdb2gmx command.
> Thank you in advance
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 129 residues with 1971 atoms
> Chain time...
> Making bonds...
> Warning: Long Bond (1459-1462 = 0.259531 nm)
> Warning: Long Bond (1754-1757 = 0.259591 nm)
> Number of bonds was 1995, now 1995
> Generating angles, dihedrals and pairs...
> Before cleaning: 5163 pairs
> Before cleaning: 5208 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...
> There are 5208 dihedrals,  429 impropers, 3556 angles
>            5127 pairs,     1995 bonds and     0 virtual sites
> Total mass 14324.281 a.m.u.
> Total charge 19.000 e
> Writing topology
> Processing chain 2 (39 atoms, 1 residues)
>
> Warning: Starting residue FLO1 in chain not identified as Protein/RNA/DNA.
> This chain lacks identifiers, which makes it impossible to do strict
> classification of the start/end residues. Here we need to guess this residue
> should not be part of the chain and instead introduce a break, but that will
> be catastrophic if they should in fact be linked. Please check your structure,
> and add FLO to residuetypes.dat if this was not correct.
>
> 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
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 1 residues with 39 atoms
> Chain time...
> Making bonds...
> No bonds
> Generating angles, dihedrals and pairs...
> Making cmap torsions...
> There are    0 dihedrals,    0 impropers,    0 angles
>               0 pairs,        0 bonds and     0 virtual sites
> Total mass 373.322 a.m.u.
> Total charge 0.000 e
> Writing topology
> Including chain 1 in system: 1971 atoms 129 residues
> Including chain 2 in system: 39 atoms 1 residues
> Now there are 2010 atoms and 130 residues
> Total mass in system 14697.603 a.m.u.
> Total charge in system 19.000 e
>
> Writing coordinate file...
>          --------- PLEASE NOTE ------------
> You have successfully generated a topology from: complex.pdb.
> The Oplsaa force field and the spc water model are used.
>          --------- ETON ESAELP ------------

There are two methods to handle this case:

1. Write an .rtp entry that encompasses both the ligand and the residue 
to which it is covalently linked, including the bond between the two 
entities. Add this new residue as Protein in residuetypes.dat.

2. As David suggested in his message, leave the ligand in a separate 
chain and deal with it as a separate species. This approach requires you 
to add an entry to specbonds.dat to generate the bond between the 
protein and the covalent ligand.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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