It was my impatience, I forgot to make install.
Afterwards I can't find any obvious error.
I will have a closer look tomorrow at all steps and let you know if I have
any questions.
Thanks for making such a valuable tool.
On Wed, Sep 30, 2020, 19:05 Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> If possible, could you say exactly what the problem was so that other
> people who might encounter this can fix it (and so if it's an issue
> with the script I can fix it). Also, since the script is very much a
> beta version, any other feedback (negative or positive) is much
> appreciated.
>
> -Dan
>
> On Wed, Sep 30, 2020 at 7:54 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> >
> > 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 script to equilibrate a
> protein+non-standard residue.
> >> As recommended, I have first installed the github version of 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 - 07:00:03 PDT
