[AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff?

From: Bikash Ranjan Sahoo <bikash.bioinformatics.gmail.com>
Date: Tue, 23 Sep 2014 17:06:31 +0900

Dear Members,
                     I am trying to simulate the DOPC_128 (
http://ambermd.org/tutorials/advanced/tutorial16/)
<https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial16%2F)>

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 : *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.

*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?



----------------------------------------------------------
*BIKASH RANJAN SAHOO (‚ÄčOsaka University)*


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Received on Tue Sep 23 2014 - 01:30:02 PDT
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