Hi Carlos,
Thanks for the reply. I am on a mac. When I attempt to load the rst7 directly into the prmtop the program prints `rst7plugin) Title: CDF` and then just hangs (for at least 90 mins so far). The rest7.pdb loads very quickly into VMD as a new molecule.
A few additional observations that may be relevant to my ‘different number of atoms’ dilemma:
It’s my understanding that the system does/should in fact contain 17,289 atoms summed from 81AAs (containing 1289 atoms), 5320 solvent molecules (i.e., 15,960 atoms), 21 Na+, and 19Cl-.
When I load the prmtop into VMD, I’m told it contains 22,609 atoms. Cpptraj agrees (22,609 atoms, 5441 residues, 5320 waters, and 5361 fragments). I am unsure of why prmtop contains 5320 (the number of solvent molecules) additional atoms relative to the 17,289 I expect.
When I load rst7.pdb in VDM it says the file contains 17,289 atoms and 5320 water molecules. When I open the rst7 in cpptraj however, I’m told it contains 22,609 atoms. In a text editor, rst7.pdb contains 22,610 atoms (according to the atom number column) and the numbering of WAT atoms looks a little weird… numbers are being skipped resulting in each WAT molecule advancing the atom count by 4 instead of by 3 (as can be seen in the snippet below). This makes me think the atom numbers are overestimating the number of water molecules by 5320.
ATOM 1330 O WAT 122 23.671 -15.591 72.581 1.00 0.00 O
ATOM 1331 H1 WAT 122 23.907 -14.797 72.308 1.00 0.00 H
ATOM 1332 H2 WAT 122 22.944 -15.756 72.128 1.00 0.00 H
TER 1334 WAT 122
ATOM 1334 O WAT 123 -13.067 44.749 129.745 1.00 0.00 O
ATOM 1335 H1 WAT 123 -13.113 45.472 130.232 1.00 0.00 H
ATOM 1336 H2 WAT 123 -13.783 44.305 129.970 1.00 0.00 H
TER 1338 WAT 123
ATOM 1338 O WAT 124 -19.637 56.031 24.132 1.00 0.00 O
ATOM 1339 H1 WAT 124 -18.984 56.608 24.101 1.00 0.00 H
ATOM 1340 H2 WAT 124 -19.579 55.613 23.368 1.00 0.00 H
TER 1342 WAT 124
Thanks
From: Carlos Simmerling via AMBER <amber.ambermd.org>
Date: Thursday, November 17, 2022 at 12:32 PM
To: Kerry Woolnough <woolnouk.uoguelph.ca>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Restart and Topology Files Contain Different Numbers of Atoms
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a few suggestions:
1) don't convert to a pdb first, just load the restart directly into VMD
after loading the prmtop first.
2) if you're on windows, and saved your restart in netcdf format, then use
cpptraj to convert it to an ascii restart (give it a file extension of
.rst7).
On Thu, Nov 17, 2022 at 12:30 PM Kerry Woolnough via AMBER <
amber.ambermd.org> wrote:
>
> Hello,
>
> In Short:
>
> When attempting to load a prmtop and restart file into VMD, I am receiving
> the error “Mismatch between existing molecule or structure file atom count
> and coordinate or trajectory file atom count”, and I’m unsure of how this
> could arise.
>
> Long Version:
>
> I am new to MD and attempting to reproduce ambermd.org Tutorial 3.1
> (Relaxation of Explicit Water Systems) using pmemd.cuda and Amber20. The
> final relaxation stage is run with the following call:
>
> $AMBERHOME/bin/pmemd.cuda -O -i 9md.in\
> -o 9md.out -p RAMP1_ion.prmtop -c 8md.rst7 -r
> 9md.rst7\
> -inf 9md.info -ref 8md.rst7 -x mdcrd.9md
>
> In ‘Step 11. Checking Relaxation’, the instructions say to load the prmtop
> and then the rst7 files into a visualization program like VMD. I converted
> 9md.rst7 to PDB, loaded RAMP1_ion.prmtop into VMD as a new molecule,
> selected ‘Load Data into Molecule’, and chose my 9md_rst7.pdb file. I
> received an error stating that the files contain different numbers of atoms.
>
> To rule out unnoticed errors that may have occurred during my relaxation
> steps, I tried instead loading the prmtop and rst7 files downloaded
> directly from the succeeding tutorial (Tutorial 3.3 Running MD with Pmemd)
> but I encountered the same error:
>
>
> ERROR) Error reading optional structure information from coordinate file
> /Users /Downloads/VMD/RAMP1_equil_rst7.pdb
>
> ERROR) Will ignore structure information in this file.
>
> Info) Using plugin pdb for coordinates from file
> /Users/Downloads/VMD/RAMP1_equil_rst7.pdb
>
> ERROR) Incorrect number of atoms (17973) in
>
> ERROR) coordinate file /Users/Downloads/VMD/RAMP1_equil_rst7.pdb
>
> ERROR) Mismatch between existing molecule or structure file atom count and
> coordinate or trajectory file atom count.
>
> Info) Finished with coordinate file
> /Users/Downloads/VMD/RAMP1_equil_rst7.pdb.
>
> I’m unclear of how the restart file could contain a different number of
> atoms than the topology file used in the pmemd run that generated the
> restart file. If anyone could shed some light on this it would be greatly
> appreciated.
>
> Thanks!
>
>
>
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>
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Received on Thu Nov 17 2022 - 12:30:03 PST
