[gmx-users] Problem with pdb2gmx

[Justin Lemkul]

On 4/11/20 2:55 PM, Elham Taghikhani wrote:
>   Thank you.
> I did what you said and added new bond to specbond.dat file like this:
> 10
> LYS     CD      2       FLO     NZ      2       1.8     LYS    FLO
> LYS     NZ      2       FLO     CX      2       1.8     LYS     FLOCYS    SG    1    CYS    SG    1    0.2    CYS2    CYS2

I don't know whether it's your email formatting or the actual content of 
specbond.dat, but make sure you're using proper line endings.

Also note that I doubt what you're doing is right. If you're simply 
asking for your residue to be bonded to NZ of LYS, that will generate a 
total of 5 bonds to NZ and not account for the change in charge. You 
should be generating a custom LYS residue and name it something else, 
which should be specified in the second-to-last column in specbond.dat. 
You will need to add it to residuetypes.dat, as well.

> CYS    SG    1    HEM     FE    2    0.25    CYS2    HEME
> CYS    SG    1    HEM     CAB    1    0.18    CYS2    HEME
> CYS    SG    1    HEM     CAC    1    0.18    CYS2    HEME
> HIS    NE2    1    HEM     FE    1    0.2    HIS1    HEME
> MET    SD    1    HEM     FE    1    0.24    MET    HEME
> CO      C       1       HEME    FE      1       0.19    CO      HEME
> CYM     SG      1       CYM     SG      1       0.2     CYS2    CYS2
>
> but it seems that it doesn't read the lines of the specbond.dat file.

Which file did you modify? One in your local directory or the 
system-wide version in $GMXLIB?

> 8 out of 8 lines of specbond.dat converted successfully...CASPH   Protein
> CGLUH   Protein
> FLO     Other

I suggested adding FLO as "Protein," not as "Other."

> DA    DNA
> DG    DNA
> DC    DNA..This is part of my residuetypes.dat file.
> I think there is some problem with my residuetypes.dat file but i don't what it is.
> nothing works i am so confused now.

Please always provide the full screen output of pdb2gmx. There is a lot 
of diagnostic information it contains that may help.

You may also want to post your PDB file and modified force field 
somewhere so we can better help in troubleshooting what is going on.

-Justin

>      On Saturday, April 11, 2020, 8:46:55 PM GMT+4:30, Elham Taghikhani <elham802011 at yahoo.com> wrote:
>   
>    Thank you for your suggestion. I gave the molecule new chain identifier and they are HETATOM in my pdb file.but still it has this warning:
>
> Warning: No residues in chain starting at FLO1 identified as Protein/RNA/DNA.
> This makes it impossible to link them into a molecule, which could either be
> correct or a catastrophic error. Please check your structure, and add all
> necessary residue names 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
>
>
>      On Saturday, April 11, 2020, 2:08:47 PM GMT+4:30, Elham Taghikhani <elham802011 at yahoo.com> 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 ------------
>
>
>      On Saturday, April 11, 2020, 1:15:38 PM GMT+4:30, Elham Taghikhani <elham802011 at yahoo.com> 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 doesn't work.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.
>      On Friday, April 10, 2020, 08:45:32 PM GMT+4:30, Elham Taghikhani <elham802011 at yahoo.com> wrote:
>   
>   Hi
>
> I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format.
> In the topology, I got this warning message :
> Warning:long-bond...
> I don't know what should I do to retain the covalent bond.
> I will appreciate it if you help me with this problem.

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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