[gmx-users] Problem with pdb2gmx
Elham Taghikhani
elham802011 at yahoo.com
Sun Apr 12 20:42:35 CEST 2020
Hi
Yes the spacbond.dat and residuetypes.dat files are in my oplsa folder in my working directory.
When it gives me topol.top file, it has another name (other_chain B) not FL.
I think thats why it doesn't recognize my ligand as a Residue.
> On Apr 11, 2020, at 11:25 PM, Elham Taghikhani <elham802011 at yahoo.com> 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 FLO
> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> 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.
>
> 8 out of 8 lines of specbond.dat converted successfully.
> .
> .
> CASPH Protein
> CGLUH Protein
> FLO 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.
> 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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