Dear Daniel,
One small-thing I already noticed that it was necessary to use the --ares
argument twice to specify two different non-standard residues which I
wanted to restrain in the initial steps.
That is --ares HM1 FE1 failed to apply restraints on the 2nd residue in the
md input files.
But using it like the following worked.
--ares HM1 --ares FE1
I hope this helps optimize the usage of different options in the next
update/release.
Please let me know if you want any other specific detail that might add
value.
Best regards
On Wed, Sep 30, 2020 at 7:23 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
--
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 - 09:30:02 PDT
