VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 25 2019 - 01:32:23 CDT

Hi,
  FYI, I have reproduced the problem you reported with your old ASCII format
AMBER, but I haven't (yet) determined what is causing it.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 20, 2019 at 06:51:17PM +0300, viktor drobot wrote:
> No, I haven't mixed up anything (in that case VMD usually alerts me
> in console).
>
>
> OK, right now I'm using AmberTools19 + AMBER18 software package. You
> can download my testcase from here
> (https://ftp.desolve.ru/ftp/viktor/vmd_mdcrd_bug.tar.gz). A brief
> explanation/details are below.
>
>
> Testcase is simple alanine dipeptide system solvated with TIP3P
> water (10 angstroms buffer from each side, so PBC are here). System
> was prepared in tleap, here is config for leap:
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> peptide = sequence { ACE ALA NME }
> solvatebox peptide TIP3PBOX 10.0
> saveamberparm peptide system.prmtop system.inpcrd
> quit
>
> Output files are system.prmtop (according to the VMD terminology
> it's "AMBER7 Parm") and system.inpcrd (I can open it in VMD if I
> choose "AMBER7 Restart"; "AMBER Coordinates" or "AMBER Coordinates
> with Periodic Box" doesn't work), latter is just plain text file (I
> can see human-readable structure in text editor). After that I've
> made some simple calculations - minimization and heating.
>
>
> Step 1. Minimization
>
> Config is:
> Minimize system
>  &cntrl
>   imin   = 1,
>   maxcyc = 10000,
>   ncyc   = 5000,
>   cut    = 10.0,
>   ntb    = 1,
>   ntc    = 1,
>   ntf    = 1,
>   ntpr   = 10,
>   iwrap  = 1,
>   ioutfm = 0
>  /
>
> Command to run (actually doesn't matter which executable is used:
> sander, sander.MPI, pmemd.cuda etc):
> mpirun -n 4 pmemd.MPI -O -i 01_min.in -c system.inpcrd -p
> system.prmtop -o 01_min.out -r 01_min.rst
>
>
> Step 2. Heating (and producing actual mdcrd)
>
> Config is:
> Heat system
>  &cntrl
>   imin      = 0,
>   irest     = 0,
>   ntx       = 1,
>   nstlim    = 50000,
>   dt        = 0.002,
>   cut       = 10.0,
>   ntb       = 1,
>   ntc       = 2,
>   ntf       = 2,
>   ntr       = 1,
>   ntt       = 3,
>   ntpr      = 1000,
>   ntwx      = 1000,
>   ntwr      = 1000,
>   nscm      = 500,
>   gamma_ln  = 3.0,
>   tempi     = 0.0,
>   temp0     = 300.0,
>   restraintmask = '!(:WAT) & !@H=',
>   restraint_wt  = 10.0,
>   nmropt    = 1,
>   iwrap     = 1,
>   ig        = -1,
>   ioutfm = 0
>  /
>
>  &wt TYPE = 'TEMP0', istep1 = 0, istep2 = 50000, value1 = 0.0,
> value2 = 300.0 /
>  &wt TYPE = 'END' /
>
> Command to run:
> mpirun -n 4 pmemd.MPI -O -i 02_heat.in -c 01_min.rst -ref 01_min.rst
> -p system.prmtop -o 02_heat.out -r 02_heat.rst -x 02_heat.mdcrd
>
> Please note that it's explicitly requested for old mdcrd format in
> both config files (ioutfm = 0). After that I have 02_heat.mdcrd file
> - it's just plain text file. However, I can't open it within my
> system.prmtop in VMD - the problem is exactly the same as described
> in my first post. You can check it by downloading my testcase
> archive and trying to visualize trajectory - neither "AMBER
> Coordinates" nor "AMBER Coordinates with Periodic Box" option works
> (in this particular case the latter option should work because I've
> prepared my testcase with PBC; however, even for simple in vacuo
> systems without PBCs the former options doesn't work too).
>
> If I convert my mdcrd to NetCDF with the help of cpptraj:
> parm system.prmtop
> trajin 02_heat.mdcrd
> trajout 02_heat.nc
> run
> quit
>
> then I'm able to open converted trajectory with my topology
> (converted trajectory is in testcase archive too).
>
> >Hi,
> > Most likely you've mixed up a restart variant vs. a trajectory
> >variant. We haven't made any changes to the plugins for reading
> >the mdcrd files, so unless you have got the wrong file type or
> >something has changed with the file structure in the particular
> >version of AMBER you're using, I don't think there's actually a
> >"bug" here. To determine what's going on, we would need to have a
> >copy of your input files, and much more extensive details about
> >how you generated them.
> >
> >Best regards,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Fri, Sep 20, 2019 at 05:41:40PM +0300, viktor drobot wrote:
> >>Ok, where I can file a bug for this issue? 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/