Dear RG members,
I am trying to simulate the DOPC_128 (http://ambermd.org/tutorials/advanced/tutorial16/)
following the steps described in Amber_16 tutorial. As I do not have access to Amber14, I am using Amber11-ff for the given lipid instead of 14 (source leaprc.lipid11 ; source leaprc.ff12SB ; loadamberparams frcmod.ionsjc_tip3p). I am very new to Amber package, and trying to follow the exact steps as mentioned in the tutorial. For trial purpose, I have sucessfuly completed up to Hold_1 (my last command : dplace -c 200-249 mpirun -n 50 pmemd.MPI -O -i 04_Hold.in -o 04_Hold_1.out -p DOPC_128.prmtop -c 03_Heat.rst -r 04_Hold_1.rst -x 04_Hold_1.nc &). This command ran successfully with expected outputs. The tutorial suggested to run hold production 10 times, however, for limited CPU power and to save time I tried to skip further hold production and tried to run Production MD using the following command.
dplace -c 200-249 mpirun -n 50 pmemd.MPI -O -i 05_Prod.in -o 05_Prod.out -p DOPC_128.prmtop -c 04_Hold_1.rst -inf -r 05_Prod.rst -x 05_Prod.nc &
The errors were
unknown flag: 05_Prod.rst
usage: pmemd [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -inf mdinfo -l logfile]
[-ng numgroups -groupfile groupfile -rem remd_method]
[-amd amdlog_name -suffix output_files_suffix]
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 38439 RUNNING AT uv
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
================================================================
Please find the attached Prod.in file (same as prescribed in the tutorial) and help me to complete the MD run.
Thanking You
Sincerely
Bikash
P.S.
Kindly share a good tutorial for protein-lipid MD simulation using Amber12. I am searching for a relevant technique (without using CHARMM-GUI ) to orient my protein in lipid (like g_membed/editconf and inflategro.pl for gromacs). How can I orient my protein in lipid bilayer for Amber package at a specified region?
You can try NAMD. It is free and good for the type of simulation you mentioned. It has very good tutorials also.
Dear Dr. Jahiruddhin,
Thank you for your suggestions. I am sorry. I want to learn Amber for other future calculations where gromacs and NAMD have substantial limitations.
Thanking you
Sincerely
Bikash
Dr. Sahoo,
It would be interesting to know the type of calculations for which NAMD fails and Amber triumphs.
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