I have a .pdb file, in this file when I want to use pdb2gmx command
> there is this error massage:
> Fatal error:
> Incomplete ring in HIS680Ask
What should to do?
i think you have to read gromac tutorial then you can do this easily
Refer the tutorial.
For this question, you can use -ignh option or you can mutate the same residue by itself.
Please see the link
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
Thank you, Vinod Kumar Jatav, Navneet Chaturvedi, Rajesh Kumar Pathak sir for suggestion.
some points i want to make clear that i have performed tutorial Lysozyme in water but
when i used another .pdf file for gmx pdb2gmx then i got this error message after selection of force field
Fatal error
Incomplete ring in HIS680.
In another .pdf file, when i used for gmx pdb2gmx and after selection of force field, i got the message
Fatal error
Residue MSE is missing form topology file
i think that probably you have a problem with topology in your pdb file.
Check the topology rules in the force field file and the edit your pdb.
Hello!
First error: Is it an edited pdb file or you took it from Protein Data Bank? In the first case check your spelling, in the second, as Navneet Chaturvedi suggested you can mutate the same residue by itself.
Second error: Which is your forcefield? All residues in your topology must be defined in the forcefield
I provided an answer on gmx-users yesterday:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-July/099472.html
The error is clearly stated. You're missing atoms and need to rebuild them with some external program. Always check your PDB files for very clear MISSING lines in the header and you will avoid surprises.
Thank you Luca Palazzolo, Hugo Ariel Alvarez, Justin Lemkul, Nixon Raj for suggestion..........
I have tried so many times but not getting solution.
I checked .pdf file which has MSE residue in it. i unable to understand why it is showing error for this.
there are some query like
How to check the .pdb file for missing line?
How to rebuild the missing atoms?
How to mutate the atom ?
You can ignore the Hydrogen atoms (-ignh flag on pdb2gmx) or add the atoms. You can add the missing H with pymol or similar.
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