From: M. A (matabay2010_at_gmail.com)
Date: Fri Feb 05 2021 - 05:26:01 CST
Dear all,
I simulated protein and ligand with NAMD successfully. Now I want to
calculate the binding free energy of this interaction with the BFEE plugin
of VMD. I have a problem when I run configure files of 001_RMSD_bound,
006_polar_phi, 007_r and 008_RMSD_unbound folders of computations. From the
kind of the error I guess it is related to the centers value that was 0.0
while the other steps executed correctly and the centers value was 0.0 for
all steps by default of the VMD.
I don't know how I can define centers value in harmonic parameters because
I konow that I should change the center value from 0.0. Could you please
help me to solve this problem?
for example: the error in 006_polar_phi step was:
*** Error in `/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2':
invalid fastbin entry (free): 0x00002ad7a8258330 ***
======= Backtrace: =========
/lib64/libc.so.6[0x31c047413e]
/lib64/libc.so.6[0x31c0479b7e]
/lib64/libc.so.6[0x31c047a31f]
/home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x129aaa9]
/home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x5fd53e]
/home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x10d1173]
/home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x1295780]
/home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x127a884]
/home/atabay.che.sharif/NAMD_Git-2019-11-26_Linux-x86_64-multicore-CUDA/namd2[0x12774a8]
/lib64/libpthread.so.0[0x31c10071f3]
/lib64/libc.so.6(clone+0x6d)[0x31c04ea9dd]
======= Memory map: ========
00400000-0d438000 r-xp 00000000 00:16 1723597063
0d637000-0d643000 r-xp 0d037000 00:16 1723597063
0d643000-0d6ab000 rwxp 0d043000 00:16 1723597063
0d6ab000-0d731000 rwxp 00000000 00:00 0
0e6d2000-18a10000 rwxp 00000000 00:00 0
[heap]
200000000-200200000 ---p 00000000 00:00 0
200200000-200400000 rwxs 00000000 00:05 383465
/dev/nvidiactl
200400000-202400000 rwxs 00000000 00:05 383465
/dev/nvidiactl
202400000-205400000 rwxs 00000000 00:05 383465
/dev/nvidiactl
205400000-206000000 ---p 00000000 00:00 0
206000000-206200000 rwxs 00000000 00:05 383465
/dev/nvidiactl
206200000-206400000 rwxs 00000000 00:05 383465
/dev/nvidiactl
206400000-206600000 rwxs 206400000 00:05 383471
/dev/nvidia-uvm
206600000-206800000 rwxs 00000000 00:05 383465
/dev/nvidiactl
206800000-206a00000 ---p 00000000 00:00 0
206a00000-206c00000 rwxs 00000000 00:05 383465
/dev/nvidiactl
206c00000-300200000 ---p 00000000 00:00 0
31c0000000-31c0021000 r-xp 00000000 08:01 788872
/lib64/ld-2.18.so
31c0220000-31c0221000 r-xp 00020000 08:01 788872
/lib64/ld-2.18.so
31c0221000-31c0222000 rwxp 00021000 08:01 788872
/lib64/ld-2.18.so
31c0222000-31c0223000 rwxp 00000000 00:00 0
31
Bests
-- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology
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