On 3/21/18 11:40 PM, Lewis Martin wrote:
To answer my own question, the MacKerell website has the correct parameter
files for GROMACS to use via pdb2gmx:
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs , put this in the
same directory.
I'm now following instructions from various gromacs mailing list posts and
tutorials. Specifically, to remove water and ions (since .itp files already
exist for these) and then run pdb2gmx. Following this, add lines like this:
#include "charmm36-jul2017.ff/tip3p.itp" for water and ions to your new
topol.top, and lines like this:
SOL 21930
NA 57
CL 63
to the [ molecules ] section.
Finally, grompp gives this error:
gmx grompp -f mdout.mdp -c myfile.pdb -p topol.top
number of coordinates in coordinate file (myfile.pdb, 114864) does not
match topology (topol.top, 118925)
How is grompp counting the number of coordinates in the topology file? It's
grompp reads the number of entries in the [molecules] directive of the
.top and multiplies each by the number of atoms in the corresponding
[moleculetype].
If you're doing manual hacking of a coordinate and/or topology file, you
have to do your own bookkeeping, and do it carefully. This error is
almost always due to simple mistakes in counting the number of species
present.
-Justin
suspiciously close to being right... But it doesn't add up to the number of
ions, lipid, water, or protein atoms. Is it just number of molecules x
number of atoms in .itp file? Should each POPC residue have a TER record
after it since they're not linked in a chain?
Thanks.
On Wed, Mar 21, 2018 at 3:04 PM, Lewis J Martin <lewis.marti...@gmail.com>
wrote:
Hi all,
I'd like to run simulations using virtual site hydrogens to allow
increased timestep. I can't find a tool for generating HMR hydrogens
(common in Amber) so Im looking at vsites.
For convenience I'm using CHARMM-GUI. Is pdb2gmx the correct tool to
introduce vsites? Using it, I keep coming across:
'Atom OT1 in residue VAL 364 was not found in rtp entry VAL with 16 atoms
while sorting atoms.'
This suggests a problem with the terminal patch, yet using the -ter flag
and choosing the terminal patch results in the same issue. Inspection of
the file 'aminoacids.c.tdb' suggests that OT1 is indeed included in the
parameters.
So I turned to other tools like psf2top and ParmEd. psf2top works
beautifully, but can't include vsites. Can you add vsites directly to
.top/gro files without pdb2gmx?
Any info is appreciated.
Cheers
Lewis
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Virginia Tech Department of Biochemistry
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