VMD-L Mailing List

From: Ethan Croitoru (ecroitoru1_at_gmail.com)
Date: Wed Aug 05 2020 - 13:30:05 CDT

Hi Josh,

When I delete the cmap section I get a new error:

ERROR: The cut-off length is longer than half the shortest box vector or
  longer than the smallest box diagonal element. Increase the box size or
  decrease rlist.

And I am not sure how to resolve this as I don't know where the box size
was set or rlist. My best guess is that these are supposed to be in the
.mdp file, but I am using a random sample one I found online, as to my
understanding this file doesn't matter that much for me, but needed for the
command. Might you know how to change these?
Also, when I try to add the parameter files, vmd just spits out

invalid command name "..."

And I am not sure what to make of that, since there is not "..." in the
command, my best guess is it comes from the list command in adding the
parameter files.
This is what my .mdp file looks like, if it helps:
integrator = md
dt = 0.002
nsteps = 500000

nstlog = 5000
nstenergy = 5000
nstxout-compressed = 5000

continuation = yes
constraints = all-bonds
constraint-algorithm = lincs

cutoff-scheme = Verlet

coulombtype = PME
rcoulomb = 1.0

vdwtype = Cut-off
rvdw = 1.0
DispCorr = EnerPres

tcoupl = V-rescale
tc-grps = Protein SOL
tau-t = 0.1 0.1
ref-t = 300 300

pcoupl = Parrinello-Rahman
tau-p = 2.0
compressibility = 4.5e-5
ref-p = 1.0

Best,
Ethan

On Wed, Aug 5, 2020 at 11:55 AM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:

> Hi Ethan,
>
> Does it work if you delete the [cmap] section from the output .top file?
> Or add in the charmm parameters for giggles when making the .top file?
> Grompp is complaining about the crossterm/CMAP correction in the psf, which
> is a perfectly normal thing for a protein model to have, but *maybe* it is
> complaining that there aren't parameters for the interaction it is trying
> to make. If neither of the first two options work for you, would you mind
> sending your inputs so I can dig a bit deeper?
>
> -Josh
>
> On Wed, Aug 5, 2020 at 9:56 AM Ethan Croitoru <ecroitoru1_at_gmail.com>
> wrote:
>
>> Hello,
>>
>> I have a NAMD simulation (i.e. dcd and psf files), and would like to use
>> some of GROMACS trajectory analysis commands. In order to do so I need a
>> sudo .tpr file, one that's good enough for analysis, but won't work for
>> simulation. I have been following the steps outlined here:
>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2003-2012/14046.html
>> So I have a .top file from using the vmd plugin topo (
>> http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/), but when I try
>> to execute this gmx grompp command:
>>
>> gmx grompp -f sample.mdp -c structure.pdb -p structure.top -o
>> simulation.tpr
>>
>> I get:
>>
>> Fatal error:
>> Unknown cmap torsion between atoms 13 15 17 23 25
>>
>> I have seen this can be an issue with the .top file used, so to create
>> that I ran:
>>
>> topo writegmxtop structure.top
>>
>> with the psf and pdb files loaded into vmd. From my understanding, I
>> don't need to add parameter files since I won't be running simulations with
>> these files.
>> Any help with this error would be appreciated.
>>
>> Best,
>> Ethan
>>
>