Charmff protein-protein decomposition analysis

[Maciej Wiśniewski]

Hi,

I'm gonna calculate the Decomposition analysis for my Protein-Protein complex.

I've already prep trajectory and calculate MMPBSA,  but now i have encountered some problems.

My command:

gmx_MMPBSA -O -i input_mmpbsa.in -cs md_0_1.tpr -ci group_indexes.ndx -cg 0 1 -ct analysis_good/traj/complex1.xtc -cp topol.top -do analysis_good/mmpbsa/decomposition_complex1.dat -deo analysis_good/mmpbsa/decomposition_complex1.csv

Input file:

&general
sys_name=""mmpbsa3csy",
startframe=5000,
endframe=10000,
interval=50,
PBRadii=7,
temperature = 310.15,
/
&pb
istrng=0.15,
fillratio=4.0,
radiopt=0
/
&decomp
idecomp=2,
dec_verbose=3,
print_res="within 4"

Error:

 At line 143 of file /home/conda/feedstock_root/build_artifacts/ambertools_1645002103866/work/AmberTools/src/sander/rgroup.F90 (unit = 5, file = '_GMXMMPBSA_pb_decomp_com.mdin')

Fortran runtime error: End of file

Error termination. Backtrace:
#0  0x7fb6967ea068 in read_sf_internal
        at ../../../libgfortran/io/transfer.c:325
#1  0x7fb6967e7d7d in read_default_char1
        at ../../../libgfortran/io/read.c:455
#2  0x7fb6967eb007 in formatted_transfer_scalar_read
        at ../../../libgfortran/io/transfer.c:1787
#3  0x7fb6967ebc66 in formatted_transfer
        at ../../../libgfortran/io/transfer.c:2491
#4  0x55aba49616b8 in ???
#5  0x55aba48eb9fa in ???
#6  0x55aba489781f in ???
#7  0x55aba4894fb6 in ???
#8  0x55aba489502e in ???
#9  0x7fb6964a7082 in ???
#10  0x55aba46c9098 in ???
[ERROR  ] CalcError /home2/sfglab/mwisniewski/anaconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!

If you are using sander and PB calculation, check the *.mdout files to get the sander error

Does anyone know how to solve this problem?

[Mario Ernesto]

Please check this thread

https://groups.google.com/g/gmx_mmpbsa/c/9eLrc0MlsME/m/fSQuM__hAwAJ

That's seems to be a reported issue on the new version that has been corrected... Pleas, let us know if this solves the issue 

--
You received this message because you are subscribed to the Google Groups "gmx_MMPBSA" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gmx_mmpbsa+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/8252d1d4-6a69-42c1-89f0-2b8a7b67f851n%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.