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 - 07:00:02 PDT
