Hi everybody!
I'm using ATB to create .itp file for gromacs MD and I have repeatedly received this error message: "the submitted molecule has a critical connectivity missing or contains more than one molecule."
I have selected ligand file from docked structure of protein and ligand which has performed by Autodock. I don't know why the file is not competent for ATB job.
The scheme of file is here:
Your file is not correct PDB format, as a result ATB likely can't parse it.
Dear Justin
Can I change it manually (A to C) if or not can I use the ligands archive in ATB for a docked complex simulation?
There are several possible problems. It is impossible to tell if the spacing is correct just from looking at an image, and most glaringly you're missing a residue name. Whether or not the last fields are even read, I have no idea. Start with the simplest fixes and checks - add a residue name, verify the column alignment through the coordinates, and try uploading it again.
Hi dears
I used ATB to creat DRG.itp and editconf command for DRG.gro files. I set a box and added ions successfully but in energy minimization i got this error:
----------------------------------------------------------
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.1#
Steepest Descents converged to machine precision in 110 steps,
but did not reach the requested Fmax < 1000.
-------------------------------------------------------------
My files are attached. Please let me know if you find any problem in them .
Thanks
There are no bonded interactions in the topology so nothing is keeping the molecule together! That is a catastrophic problem. The charges also look a bit weird to me; compare with known functional groups already in the force field. Aromatic -OH and alkyl-linked -NH3+ are all well defined in the force field. Everything here should be fairly boilerplate cut-and-paste from existing functional groups.
I have set the net charge with +1 for hydrogenated ligand. Does it make the problem for the charges calculation?
Thank u is not enough for all your supports Justin.
I didn't understand what is your main problem? If you couldn't do energy minimization with large number of step size you can continue your MD simulation without doing this step. Please don't worry about missing energy minimization process.
Thanks for your answer Mr. Barzegar
Actually I'm concerned if it could make indiscernible problem in future steps.
However I will follow your advice.
Mr. Barzegar
In response to your advice about ignoring energy minimization step, I do NVT equilibration. Now I get this fatal error:
"13 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated."
It seems that there is a problem in topology file as before.
I have attached the nvt.mdp file and any new suggestion is welcomed.
The DRG.itp that you posted before has catastrophic problems, as I pointed out. Have those been rectified? Do you have sensible bonded interactions defined?
In the .mdp file, for Gromos force fields, rvdw should be 1.4. I don't know if this is the source of the problem, but you should not deviate from the cutoffs used in the force field derivation.
Further troubleshooting should be done in accordance with http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. Be scientific - break the system down into simple parts (ligand in vacuo - is a simulation stable? ligand in water - is that stable? etc).
Thank you for valuable advices.
Of course I fixed the files.In addition,I have used that rvdw number for protein in water simulation with no problem.
I guess I should follow the tips in the link.
THANKS
How you have prepared your initial file for ATB? I propose to prepare your ligand MOL file with different softwares such as autodock Tools, pymol, sybyl, hyperchem, gaussview and then submit to ATB. Of course some of them are not compatible for ATB.
- Badges
- Science topic