FYI, I'm now able to fix the installation issue and will get back to you if
I any further questions on analyzing the data.
thank you.
On Wed, Sep 30, 2020 at 12:19 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> 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
>
>
--
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 - 05:30:02 PDT
