Dear all
I have been trying to simulate a cholesterol membrane built with the charmm membrane builder in gromacs 2019. I have tried using various forcefields to start wit the first step of minimisation as described in various online tutorials including the KALPc, but am unable to do so. the first error is the residue type not found in the topology database. then is the proper dihedrals not found. I tried OPLS, AMBER99SB and Gromos53A6 but somehow the error persists. I downloaded the cholesterol parameter files for gromacs from the charmm website.
has anybody done the simulation and can help me with it. i have another system with cholesterol:popc 40:60. there also cholesterol parameters are creating issues.
Any help is greatly appreciated. I am attaching my files for amber99sb that i modified.
thank you
Using CHARMM-GUI could be the most feasible way to simulate such system.
Ayesha Fatima you haven't indicated the correct pathway for the bonded and non-bonded parameters. In your topology file gromacs load basic parameters of amber99sb_lipid.ff/forcefield.itp but in this file parameters of CHOL is missing. there are two options to handle this issue. 1) You have to copy bonded and nonbonded parameters from the amber force field (/usr/share/gromacs/top/amber..... ) to the current folder and copy CHOL parameters to the ffnonbonded.itp and ffbonded.itp files.
Then, you should modify your topology because it loads parameters locally:
2nd line - #include "forcefield.itp"
2) Copy CHOL parameters to the database of amber (/usr/share/gromacs/top/amber..... again to the ffnonbonded.itp and ffbonded.itp files) after integrating it keep your topology as it is.
If you have questions just let me know
Hello Jamoliddin
The problem still persits. I am copying my files that I modified but the error is the same.
Fatal error:
Residue 'CHL1' not found in residue topology database
I did as you told but the file content is very different from the ones in lipids. It has only numbers as you will see in the dihedrals section of the cholesterol.itp file.
I am sure I am doing something wrong but just cant wrap it around my head
I will appreciate your help
Thank you
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