Dear all,
I have tried everything on the smiling list to simulate the cholesterol membrane. but nothing seems to work. The error is grompp
NO default proper dihedrals, no default UB types. Since the system is built on charmm gui, i have to use the charmm forcefield as the atom types match correctly.I used the Charmm36 March 2019 release and the error is
Fatal error: Syntax error - File cmap.itp, line 4 Last line read: '[ cmaptypes ]' Invalid order for directive cmaptypes
I checked the cmap types files but I cannot understand what is the error.
when I use charmm27 from Gromacs, there is no such error but the default errors are there.
I am not sure what am I doing wrong here, why I cannot set it up even. I have followed almost a;; tutorials on the net. since no one is simulating cholesterol membrane. the exact problem I am unable to identify.
I used other force fields also such as gromos 54a7 as the cholesterol itp can be obtained from the ATB server which is compatible but the error of default types. but it gives only 29 atom types for cholesterol, while the membrane has 74 atoms per cholesterol molecules, including the hydrogens. Here the error is more strange. it tells me my number of coordinates is less in topology file but I checked it is all correct (128 chol: 3130 water). the other errors are no proper dihedrals in the cholesterol.itp and default UB error. Similar issues are occuring with 53a6 and OPLSS-AA.
another common error is "Something is wrong in the coordinate formatting of file chl1.gro. Note that gro is fixed format (see the manual)" I checked the other tutorial files such as DPPC. similar lines are there, except, the cholesterol has hydrogen names A, B , C.
Can someone help me diagnose the issue here. is it the system, or the forcefields or the cholesterol itp file generated. I am attaching some of the files here. Please help, this is now become emergency.
the cmaptypes is from Charmm36.
Thank you
I shall remain grateful, if someone can help me.
Ayesha Fatima
will be difficult to help you with only a .gro... As I understand, you wanna built a cholesterol membrane, right? I built a cholesterol membrane in charmm-gui (128 molecules in each of the leaflet) and everything was good... see attached the .zip containing all the files...just make the proper changes (i.e. depending how you compiled gromacs will be gmx, gmx_mpi, gmx_d or gmx_mpi_d) in the README file and execute it with csh...
csh README
hope this helps!
Thanks Mario, I have already built the membrane using the membrane builder on charm-gui and now I want to further equilibrate is using gromacs as my next step is pulling a protein through which is prepared using gromos 54a7.
I downloaded the cholesterol.itp from the slipids home page and it had all the atom types used by the membrane builder.
i made the topology file as usual and added the colesterol itp file in it. there is no recommendation to add the lipid parameters to the gromos forcefiled, i however did it like we do for dppc and popc.
the first step as i did for dppc was to generate the gro file and tpr for minimisation.. the problem starts here. messages run for all the 128 cholesterols that "no proper dihedrals and default ub parameters are found" . I read on the gromacs mailing list that i should develop a cholesterol gro file without water which i did. when i run the command again, same issue.
Thank you for sharing the files. I see the charmm2gmx name of the file. is that an actual command or the charmm gui does that? also the charmm 36.itp file. where do we get that? when i downloaded the charmm36 file from the Mackerel website, it gave me several files. this definitely means i was using the wrong approach.
i will try using your files. and tell you. thank you once again
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