Thank you David,
I process the box boundry using equil trajectory mdcrd file to generate a correspoding nc file due to a partition of water moleculare out of box after equilation, and then open the nc file in the vmd, and select parameters "save coordinate,fist 499, last 499, stride 1" and save as DLF-equil-499.pdb file as QM/MM inuptfile (but box is gone from here) when the runing box stop, and then a new prmtop and incrd were generated from DLF-equil-499.pdb, I presume this is the case where the issue occured, but I do not know how to fix the issue, please help me, thank you.
Process the box boundry file re_image.in
_________________________
parm DLFae4-MFA-complex-wat.prmtop
trajin DLFae4-MFA_equil.mdcrd
center :1-339
image center familiar
trajout DLFae4-MFA-wat_equil_reimaged.nc
_________________________________________
cpptraj -i re_image.in
a new prmtop and incrd file generating file
---------------------------------------------------
tleap -f oldff/leaprc.ff99SB
>source leaprc.gaff
>source leaprc.water.tip3p
>loadamberparams MFA.frcmod （ligand）
>loadoff MFA.lib
>com = loadpdb DLF-equil-499.pdb
> charge com
> addions com Na+ 0
> saveamberparm com DLF-equil-499.prmtop DLF-equil-499.inpcrd
> quit
-------------------------------------------------------
Zhihong Xin
> -----Original Messages-----
> From: amber-request.ambermd.org
> Sent Time: 2020-07-28 03:00:01 (Tuesday)
> To: amber.ambermd.org
> Cc:
> Subject: AMBER Digest, Vol 3076, Issue 1
>
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>
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: Issue about "... . RESTARTED DUE TO LINMIN FAILURE..."
> (David A Case)
> 2. Re: Maximum system size (David A Case)
> 3. Amber20 Compiling problem with b2 and Boost.Regex (Amanda Buyan)
> 4. Charges for modified DNA base at the termini? (Kenneth Huang)
> 5. Re: Amber20 Compiling problem with b2 and Boost.Regex
> (David A Case)
> 6. Error building Amber (Walton Smith)
> 7. Re: Error building Amber (David A Case)
> 8. Re: Error building Amber (David A Case)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 26 Jul 2020 20:44:15 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN
> FAILURE..."
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20200727004415.mlqxwocrdmxpvyix.pop-os.localdomain>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> On Sun, Jul 26, 2020, ??? wrote:
> >
> >I extract the last frame (499 frames) of the equil pdb outfile as the
> >QM-MM input file, and regenerate prmtop and Inpcrd file, but I found that
> >the BOX coordinates in the inpcrd file are gone,
>
> Something went wrong here, and you should investigate. You don't say how you
> extracted the last frame, nor how you regenerated the prmtop and incrd file.
>
> But if you do that correctly, the box information should not be lost.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 26 Jul 2020 20:57:50 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Maximum system size
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20200727005750.oa4uunwn44luzetz.pop-os.localdomain>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Sun, Jul 26, 2020, Jack Shepherd wrote:
> >
> >Making a big system for simulation with pmemd.cuda recently I got the
> >error c must be smaller than 10^4 angstroms and nfft3 must be between
> >certain values.
>
> The maximum value for nfft1,2,3 is hard-coded in mdin_ewald_dat.F90 (see the
> gridhi variable), and the maximum box size is in boxhi (as 1000. Ang, not
> 10000 Ang., and least as I read the code.)
>
> I know that people have doubled the gridhi value, and you might experiment
> with making gridhi and boxhi larger. I'm not sure how these values will
> carry over to pmemd.cuda, but you can experiment: run short simulations with
> CPU first, then make sure you get equivalent results on the GPU.
>
> Once you get a very big system volume, the number of atoms is likely to become
> more of a limitation than is the size of the box or the number of PME grid
> points. Don't expect this to be straightforward: a cubic box of water
> with sides of 1000 Ang. would have 33 million molecules, or 100 million atoms.
> This is well beyond the expected range of Amber simulations, and generally
> requires both specialized hardware and software.
>
> ....dac
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 27 Jul 2020 01:35:07 +0000
> From: Amanda Buyan <Amanda.Buyan.anu.edu.au>
> Subject: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <SYBP282MB020247875ADC0D20EC5644E2A9720.SYBP282MB0202.AUSP282.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi everyone,
>
> Thanks for your suggestion on removing the PLUMED library - it helped! I have another question, as I'm installing Amber20 on multiple clusters:
>
> I'm currently having trouble with compiling even the serial version of Amber20 on the second cluster of ours. When I run the "make install" command (following the same procedure as on the other cluster), I get the following error:
>
> ---
> Building Boost.Build engine with toolset gcc... tools/build/src/engine/bin.linuxx86_64/b2
> Detecting Python version... 3.6
> Detecting Python root... /usr
> Unicode/ICE support for Boost.Regex?... not foud.
> Generating Boost.Build configuration in project-config.jam...
>
> Bootstrapping is done. To build, run:
>
> ./b2
>
> to adjust configuration, edit 'project-config.jam'.
>
> [ Further information about boost.build]
>
> /bin/sh: cmake: command not found
> make[2]: *** [AmberTools/src/boost/Stamp/boost_build/boost_build-bootstrap] Error 127
> make[1]: *** [AmberTools/src/boost/CMakeFiles/boost_build.dir/all] Error 2
> make: *** [all] Error 2
> ---
>
> I try to find the program b2, but I can't find any installation for it (it might have been on the other cluster, but I'm not sure). How do I check this? Do you have any advice on how to get past this step?
>
> Thanks in advance for your help.
>
> Best wishes
>
> Amanda
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 27 Jul 2020 02:50:39 -0400
> From: Kenneth Huang <kennethneltharion.gmail.com>
> Subject: [AMBER] Charges for modified DNA base at the termini?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CALeh7kCs9D6bzk=OYrq5QZkqDxO2fEAjOrQScUE6R+y74XpKPg.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi all,
>
> Something of a procedural/background question- what is the exact procedure
> for determining the charges for modified/unnatural bases at the 5'/3'
> termini?
>
> Given the termini are unique, ie their charge is non-integer by design, the
> closest I could find is the tutorial here (
> https://ambermd.org/tutorials/advanced/tutorial1/section1.htm), but trying
> to follow it as close as possible in AmberTools16 with a test run of
> something simple of native DG3' nets an EOF runtime error-
>
> resp -O -i dg_resp.in -o dg_resp.out -p dg_resp.pch -t dg_resp.chg -q
> > dg-resp1.qin -e dg_esp1.esp
> > At line 744 of file resp.F (unit = 5, file = 'dg_resp.in')
> > Fortran runtime error: End of file
> >
>
> Which I've figured has something to do with how my group constraints are
> formatted?
>
> ...etc
> > 1 0
> > 34 -0.6921
> > 1 1 1 2 1 3 1 4 1 5 1 6 1 7
> > 1 8
> > 1 9 1 10 1 11 1 12 1 13 1 14 1 15
> > 1 16
> > ...etc
> >
>
> But I can't see anything that's obviously wrong about it, or did I
> misunderstand how the group constraint is meant to work?
>
> Or am I going about this the entirely wrong way? I know in the case of DNA
> forcefields, the charges have been relatively fixed since ff94/99- so could
> I approach it as an internal base, ie do the ESP/RESP fitting on just the
> modified base portion with a methyl cap, and 'stitch' the backbone/sugar
> from the source forcefield back together for a complete base?
>
>
> Best,
>
> Kenneth
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 27 Jul 2020 09:10:37 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20200727131037.waj5o5yims736ped.pop-os.localdomain>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> On Mon, Jul 27, 2020, Amanda Buyan wrote:
> >
> >I'm currently having trouble with compiling even the serial version of
> >Amber20 on the second cluster of ours. When I run the "make install"
> >command (following the same procedure as on the other cluster), I get the
> >following error:
> >
> >---
> >Building Boost.Build engine with toolset gcc... tools/build/src/engine/bin.linuxx86_64/b2
> >Detecting Python version... 3.6
> >Detecting Python root... /usr
> >Unicode/ICE support for Boost.Regex?... not foud.
> >Generating Boost.Build configuration in project-config.jam...
> >
> >Bootstrapping is done. To build, run:
> >
> >./b2
> >
> >to adjust configuration, edit 'project-config.jam'.
> >
> >[ Further information about boost.build]
> >
> >/bin/sh: cmake: command not found
>
> I think this is the problem: you have to have cmake in your PATH: it's not
> enough to just specify the location in the run_cmake script.
>
> This is not documented in our installation instructions. And, it might not be
> the only problem. But check on the second cluster to see if cmake is in your
> PATH.
>
> ...dac
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 27 Jul 2020 10:04:33 -0400
> From: Walton Smith <smit7450.mylaurier.ca>
> Subject: [AMBER] Error building Amber
> To: amber.ambermd.org
> Message-ID: <3A1E27EB-7D19-46E4-B5DB-814F47518094.mylaurier.ca>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> I?m having trouble with building AMBER. After I ./run_cmake in terminal, the configuration never runs to completion. Here is the error log and output log associated with my difficulties. Please let me know what I can do to fix this issue, I would greatly appreciate it. Just to let you know, I?m not very familiar with terminal so this is all pretty new to me.
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 7
> Date: Mon, 27 Jul 2020 13:15:14 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Error building Amber
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20200727171514.m22a4eqpjexzyy7o.oq-fs-191g302-a.rad.rutgers.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> On Mon, Jul 27, 2020, Walton Smith wrote:
> >
> >
> > I?m having trouble with building AMBER. After I ./run_cmake in terminal,
> > the configuration never runs to completion. Here is the error log and
> > output log associated with my difficulties. Please let me know what I can
> > do to fix this issue, I would greatly appreciate it. Just to let you know,
> > I?m not very familiar with terminal so this is all pretty new to me.
>
> The most helpful file to post is "cmake.log", which is created when you
> use the "run_cmake" script. It also helps to give information about
> your operating system and environment. It looks like you are using OSX,
> but (a) which version? and (b) do you have any extra tools installed,
> such as homebrew or macports? Did you do anything unusual in
> installation, that is beyond what is suggested here?
>
> https://ambermd.org/InstMacOS.php
>
> ...thanks...dac
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 27 Jul 2020 13:48:48 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Error building Amber
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <20200727174848.zh4vutjc5fjkrpih.oq-fs-191g302-a.rad.rutgers.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> On Mon, Jul 27, 2020, Walton Smith wrote:
> >
> >
> > I?m having trouble with building AMBER. After I ./run_cmake in terminal,
> > the configuration never runs to completion. Here is the error log and
> > output log associated with my difficulties. Please let me know what I can
> > do to fix this issue, I would greatly appreciate it. Just to let you know,
> > I?m not very familiar with terminal so this is all pretty new to me.
>
> It's best to post the "cmake.log" file that is created by run_cmake.
>
> Also, let us know about your operating system and configuration. It
> looks like you are using OSX, but which version? and is there anything
> odd about your setup (is homebrew or something like that installed)?
> What do you have (if anything) in your /usr/local/lib folder?
>
> ...thanks....dac
>
>
>
>
> ------------------------------
>
> _______________________________________________
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>
>
> End of AMBER Digest, Vol 3076, Issue 1
> **************************************
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Received on Mon Jul 27 2020 - 19:00:03 PDT
