Dear Daniel and Amber community,
I'm trying to use the AmberMdPrep <
https://github.com/drroe/AmberMdPrep>
script to equilibrate a protein+non-standard residue.
As recommended, I have first installed the github version of cpptraj
<
https://github.com/Amber-MD/cpptraj> and sourced it (as suggested at the
end of the installation).
The AmberMdPrep script seems to be working well, but in the last step it is
unable to pick the right installation of cpptraj as shown below.
Can you please suggest me how to fix this and make the script use the
correct cpptraj version?
Thank you and best regards.
(base) [exx.c107739 test-AmberMDprep]$ source
/home/exx/Downloads/cpptraj-master/cpptraj.sh
(base) [exx.c107739 test-AmberMDprep]$ AmberMDPrep -p ../1HGA_solv.prmtop
-c ../1HGA_solv.inpcrd --ares HM1 --ares FE1 -O --temp 310
AmberMdPrep.sh Version 0.2 (beta)
140 protein, 0 dna, 0 rna, 0 lipid, 0 carbohydrate, 6302 water, 4 other
Unknown residues names: Cl-,FE1,HD1,HM1
Detected additional res mask: :FE1,HM1&!.H=
Warning: Unknown residues detected; will be ignored for restraints.
Detected types : protein
Orthogonal box detected.
TOP : ../1HGA_solv.prmtop
CRD : ../1HGA_solv.inpcrd
NUM SOLUTE RES : 140
HEAVY MASK : :1-140&!.H=
BACKBONE MASK : :1-140.H,N,CA,HA,C,O
ADDITIONALMASK : :FE1,HM1&!.H=
ADD. MASK RES. : HM1 FE1
TEMPERATURE : 310
OVERWRITE : 1
MD COMMAND : pmemd.cuda
MIN COMMAND : pmemd.cuda_DPFP
NPROCS : 4
Performing standard min/equil
Minimization: step1
MD: step2
Minimization: step3
Minimization: step4
Minimization: step5
MD: step6
MD: step7
MD: step8
MD: step9
Starting final density equilibration.
/usr/local/amber18/bin/cpptraj does not support density plateau evaluation.
Only running one round of final density equilibration.
Final 1
MD: final.1
*Skipping final density evaluation.*
Complete.
Equilibration success
(base) [exx.c107739 cpptraj-master]$ ./configure -amberlib gnu
Testing C++ compiler: OK
Testing C compiler: OK
Testing Fortran compiler: OK
Testing basic C++11 support: OK
Testing system headers for C++11 support: OK
Using blas from /usr/local/amber18
Using lapack from /usr/local/amber18
Using netcdf from /usr/local/amber18
Checking BZLIB: OK
Checking ZLIB: OK
Checking NetCDF: OK
Checking LAPACK/BLAS: OK
Checking for FFTW3 from AMBERHOME: OK
Checking for sanderlib: OK
Configuration summary:
Build type: Serial
Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile
sanderlib
Target platform: Linux, 64-bit.
gnu compilers in use.
C++11 support enabled.
PME support enabled.
Compiler optimizations are on.
Cleaning source directory.
--------------------------------------------------------------------------------
An environment resource file for CPPTRAJ has been created:
/home/exx/Downloads/cpptraj-master/cpptraj.sh
You may 'source' this file to set up your environment for CPPTRAJ.
--------------------------------------------------------------------------------
CPPTRAJ configuration complete.
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
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Received on Wed Sep 30 2020 - 04:00:02 PDT
