Command line:
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr
Ignoring obsolete mdp entry 'ns_type'
NOTE 1 [file minim_inflategro.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 2146958069
Generated 165 of the 1596 non-bonded parameter combinations
ERROR 1 [file dppc.itp, line 16]:
Atomtype CH3L not found
There was 1 note
-------------------------------------------------------
Program: gmx grompp, version 2021.2
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1409)
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Dear Amit Chaudhary
From the error it seems to me that you are following this tutorial
http://www.mdtutorials.com/gmx/membrane_protein/index.html
The error means what it says, that is the atom type is not recognized. This means that the atom name CH3L in the dppc.itp file was not found in the forcefield files, and GROMACS is not able to compute the corresponding quantities.
If you are following the tutorial then you made a mistake in the section where you are adding the Berger parameters in GROMOS ff, and need to go back to that step and fix it.
Hi,
if using 54a7, change to CH3p. If using 53a6, probably you have to add the extra itp file for DPPC atoms at the beginning of the topol.top file (after gromos53a6.ff/forcefield.itp)
Nicola Piasentin Running now. Thank you!
Ricardo J Ferreira Atoms added. Now running. Thank you!
Nicola Piasentin I got another error in next step,
Could you help me to resolve this.
Command used- gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 6538)
does not match topology (topol.top, 138)
Hi Amit Chaudhary ,
you probably did not add the number of DPPC molecules in topol.top file. It should be 128 DPPC molecules if using a small DPPC patch.
Just add to the [ molecules ] section:
DPPC 128
But, for information only, you have another method to embed proteins in membranes: using the gmx membed available in GROMACS.
Dear Amit Chaudhary
The numbers sound suspicious.
Check the topology, you should have the both the protein and the lipid patch.
Secondly, before energy minimization, check the number of removed lipids from the perl script and update the topology coherently (that is remove the number of DPPC molecules that the script takes away to position the protein).
If these don't work then probably the problem is in the passage where you cat the protein box with the lipid box! If you uploaded the topology and the .gro of the system it would be easier to check the problem
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