VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Wed Aug 05 2020 - 13:45:27 CDT

Hi Ethan,

Looks like you still have VMD 1.9.3, without the fix for the typo in the
tcl source:
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28199.html

Now, the new error is because grompp is trying to read a box dimension from
the input pdb file. Sometimes this works, if the box information is on the
first line of the file, but oftentimes its not, and I'm betting that is
what is going wrong here. Then you'd need to use gmx editconf to add box
information to the structure that grompp gets. It'd be something like:

gmx editconf -f input.pdb -o output.gro -box 4.0 4.0 4.0

Assuming a 40 Angstrom box edge length (Gromacs uses nm). Then you'd feed
grompp output.gro instead of the pdb without box information.

-Josh

On Wed, Aug 5, 2020 at 12:30 PM Ethan Croitoru <ecroitoru1_at_gmail.com> wrote:

> 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
>>>
>>