I am following http://www.mdtutorials.com/gmx/complex/index.html
However, there are multiple errors.
After reaching the Adding Ions step (http://www.mdtutorials.com/gmx/complex/04_ions.html), I am encountering the following output:
After running - gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
-------------------x---------------x-------------x--------------
Ignoring obsolete mdp entry 'title'
NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to -1853572670
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
ERROR 1 [file UNK.itp, line 4]:
Atomtype H842 not found
There was 1 note
-------------------------------------------------------
Program: gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1390)
Fatal error:
There was 1 error in input file(s)
------------------------------------------------------
I have obtained my ligand .gro and .itp from LibParGen and have added them in the topol.top as insctructed. the protein pdb2gmx has been obtained using the OPLS-AA ff. I have removed the .prm file from the above output as:
- I was getting an error as GROMACS was unable to read the file
- the prm file was under CHARMM/NAMD in the LibParGen Output
Thanks for any help!!
check your topol.top file, perhaps there is some issue with the name of the ligand.
Define atom type H842 or assign an already defined atom type to that hydrogen.
The error is suggesting that grompp doesn't recognize the declared [atomtype] in UNK.itp
. ........................................................................
Generated 330891 of the 330891 1-4 parameter combinations
ERROR 1 [file UNK.itp, line 4]:
Atomtype H842 not found
..........................................................................
In UNK.itp if [atomtype] is declared before [molecule] such error may occur.
Have a look at the discussion on such error at-
https://www.mail-archive.com/[email protected]&q=subject:%22Re%5C%3A+%5C%5Bgmx%5C-users%5C%5D+Invalid+order+for+directive+atomtypes%22&o=newest&f=1
My suggestions are-
1. From LigParGen Server download the GROMACS GRO and and TOP files only. (and not the PRM file which is for CHARMM ff).
2. Rename the downloaded UNK.top as UNK.itp
3. Edit the topol.top file and declare the [atomtype] before protein [moleculetype]. This you can do by inserting ; Include statement for ligand at the beginning of topol.top file. Have a look at this one.
; Include forcefield parameters
#include "./oplsaam.ff/forcefield.itp"
; Include ligand topology
#include "UNK.itp"
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
And at the end insert line for UNK
4. I assume you are using OPLS-AA while generating topol.top through pdb2gmx.
Hope this helps
Regards
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