[gmx-users] Problem with pdb2gmx

[Justin Lemkul]

On 4/12/20 2:42 PM, Elham Taghikhani wrote:
> Hi
> Yes the spacbond.dat and residuetypes.dat files are in my oplsa folder in my working directory.

These files should be in the working directory, not in the force field 
subdirectory. This is why they are not being read.

> 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.

Merge the chains with the -merge command.

-Justin

>
>> 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.

-- 
==================================================

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

Virginia Tech Department of Biochemistry
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