Re: [AMBER] namd-l: MMPBSA calculation using NAMD

From: sunyeping <>
Date: Mon, 16 Sep 2013 14:35:03 +0800

During ambertools13 install, the update is intalled automatically and it went ok during my installation.
Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

------------------------------------------------------------------发件人:Aron Broom <>发送时间:2013年9月16日(星期一) 13:52收件人:孙业平 <>抄 送:AMBER Mailing List <>主 题:Re: [AMBER] namd-l: MMPBSA calculation using NAMDI'm not sure. I've only installed up to AMBERTools 12, and it wentsmoothly. Maybe post to the amber mailing list and see what they have tosay. They'll generally first get you to ensure you've installed all theupdates.On Mon, Sep 16, 2013 at 12:56 AM, sunyeping <> wrote:> Dear Dr. Broom,> Thank you for your reply. I want to install ambertools 13 onto my centos> 5.9 system, but when I enter make command, it returns lots of error> messages relevent fftw3 as following:>>> error: sententce (1) not defined in file fftw3.f03:1732> included in * fftw3.F90*:10> type(C_PTR), value :: output_file> 1> error: Derived type 'c_ptr' at (1) is being used before it is defined in> file fftw3.f03:1733> included in fftw3.F90:10> end subroutine fftwl_export_wisdom_to_file> 1> error: need END INTERFACE ,in (1)> in file fftw3.f03:1735> included in fftw3.F90:10> type(C_PTR) function fftwl_export_wisdom_to_string() bind(C,> name='fftwl_ex> 1> error: Derived type 'c_ptr' at (1) is being used before it is defined> in file fftw3.f03:1736> included in fftw3.F90:10>>> make[2]: *** [fftw3.o] error1> make[2]: Leaving directory> `/home/hjkx/program/amber12/AmberTools/src/pbsa'> make[1]: *** [serial] error 2> make[1]: Leaving directory `/home/hjkx/program/amber12/AmberTools/src'> make: *** [install] error 2> It seemed ok when I installed fftw3, do you know how these errors occur?>> Best Regards,>> Yeping Sun>> Institute of Microbiology, Chinese Academy of Sciences> ------------------------------------------------------------------> 发件人:Aron Broom <>> 发送时间:2013年9月16日(星期一) 09:21> 收件人:孙业平 <>>> 主 题:Re: namd-l: MMPBSA calculation using NAMD>> I haven't used it extensively but when I did, yes, I used AMBER> parameters with NAMD (its what I usually do anyway). You can convert> NAMD's DCD output to AMBER's using cpptraj (part of ambertools) or even> VMD. Since the trajectories in both software packages are just lists of> coordinates. I'm not sure how well it will work if you try to convert from> a CHARMM forcefield to an AMBER one (i.e. using CHAMBER).>>>> On Sun, Sep 15, 2013 at 8:54 PM, sunyeping <> wrote:>>> Dear Dr. Broom,>> In order to use MMPBSA as one of AmberTools, do I have to apply amber>> force field when doing NAMD? Can AmerTools read dcd file generated in>> charmm force field?>>>> Best Regards,>>>>>> Yeping Sun>>>>>> Institute of Microbiology, Chinese Academy of Sciences>> ------------------------------------------------------------------>> 发件人:Aron Broom <>>> 发送时间:2013年9月16日(星期一) 06:49>> 收件人:sudipta <>>> 抄 送:NAMD <>>> 主 题:Re: namd-l: MMPBSA calculation using NAMD>>>>>> Some of the better put together MMPBSA tools are included in the free>> AMBERTools package. MMPBSA and MMGBSA are post-processing methods, so you>> can run the simulation in NAMD, save the DCD output reasonably often, and>> then do the analysis in AMBERTools, provided you are careful about setting>> the parameters to match what NAMD would have used during the simulation.>>>> ~Aron>>>>>> On Wed, Sep 11, 2013 at 8:37 AM, sudipta <> wrote:>>>>> Hi All,>>>>>> Can anyone give some suggestions how do I perform MMPBSA calculation in>>> combination with alanine scanning using NAMD?>>>>>> Best>>> Sudipta>>>>>>>>>>> -->> Aron Broom M.Sc>> PhD Student>> Department of Chemistry>> University of Waterloo>>>>>> --> Aron Broom M.Sc> PhD Student> Department of Chemistry> University of Waterloo>-- Aron Broom M.ScPhD StudentDepartment of ChemistryUniversity of Waterloo_______________________________________________AMBER mailing listAMBER.ambermd.org
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Received on Mon Sep 16 2013 - 00:00:03 PDT
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