Dear Daniel,
I have used this tool for 4-5 structures now and didn't encounter any
obvious errors or problems.
I have another question though, related to the option --nprocs.
Since most of the min and MD jobs are run on the GPU with pmemd.cuda, I'm
assuming that the script assigns these CPUs only for the analysis performed
by cpptraj (github/AmberTools version).
Nonetheless, I observed that only 1 CPU is used even if I assign > 4
(default) values.
I'm just trying to understand how to figure out the optimum usage (CPU/GPU)
in case I need to run this script for a significant number of structures.
Can you please find time to suggest on this aspect?
Looking forward to your valuable suggestions.
Thank you and best regards
Vaibhav
On Thu, Oct 1, 2020 at 1:00 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> 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
>>> >
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> 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
>
>
--
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 Fri Oct 09 2020 - 21:30:02 PDT
