Hello all
I have to do Protein - Ligand MD simulation.
Thus I am doing tutorialfor Protein - Ligand tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html
I have used following command:
pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc
editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
I am getting stuck at last command. Its showing following error:
Fatal error:
number of coordinates in coordinate file (solv.gro, 33049)
does not match topology (topol.top, 33064)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Then I trade to reduce the waters ((33064-33049)/3=5)). But it didn't help.
I obtained:
Fatal error:
Too many warnings (2), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
I want to know how to fix this problem ?
You didn't correctly adjust the second line of conf.gro after adding more atoms. Thus, when you run editconf, it reads only the first 1693 atoms, hence why you lose the ligand.
Your topology has 15 more atoms than the coordinate file. There are 15 atoms in the ligand. I suspect you forgot to paste the ligand coordinates back into the protein coordinate file before setting up the box.
You forgot using ligand topology files. You must first take a ligand topology files and combine with protein topology files.
Thanks for your answers.
I pasted the ligand coordinates back into the protein (attached file: conf.gro, ligand topology file: drg.itp).
Also I did changes in topol.top.
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include ligand topology
#include "drg.itp"
; Include water topology
#include "gromos43a1.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "gromos43a1.ff/ions.itp"
[ system ]
; Name
HYDROLASE in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
JZ4 1
Please show me where I made mistake
You didn't correctly adjust the second line of conf.gro after adding more atoms. Thus, when you run editconf, it reads only the first 1693 atoms, hence why you lose the ligand.
Hi Vasyl,
May i know that did you solve the error ? Is it working now? Because I am getting the same error so could please help me regarding the same?
I having 16 atoms extra i.e. number of coordinates in coordinate file (complex_sol.gro, 7742382) does not match topology (topol.top, 7742366). Should I still go ahead and delete 5 SOL atoms?
Hi Thank you for the reply. I got the solution. I am running it successfully. Thank you once again for the response
@ Jayaram Chikkerur
Sir I am also having the same error . kindly let me know how did u solve it
- Badges
- Science topic