[gmx-users] Converting top or tpr to psf
jalemkul at vt.edu
Sat Jan 13 01:34:31 CET 2018
On 1/11/18 10:24 AM, jamesmkrieger at gmail.com wrote:
> Thanks Justin. It’s two protein chains, water and NaCl but there are virtual sites and CMAP (charmm27 ff). I generated the full topology with grompp so yes please could I try your script. Would CHARMM-GUI or VMD be able to generate the CMAP?
Yes, anything in CHARMM will support CMAP; I was only indicating that
the application for which I developed my conversion script didn't
require it, though it would be simple to add.
Virtual sites are another matter. My script doesn't deal with those at
all (nor would it be easy to do, as the representation in GROMACS and
CHARMM format is wildly different) and if they're custom sites, then no
tool will do a PSF conversion/creation without manual creation of e.g.
CHARMM RTF files and using CHARMM directly. If you need further advice
on that, we can take this discussion off-list.
> Best wishes
>> On Jan 11, 2018, at 8:08 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>> On 1/10/18 9:47 PM, jamesmkrieger at gmail.com wrote:
>>> Does anyone have any experience with creating a psf file from a gromacs topology? I have a collaborator who uses NAMD and they are going to analyse some of my gromacs simulations together with some of their simulations but need psf files to do that.
>> I have a script that does this for very simple cases (e.g. full topology, no #include statements, also doesn't convert stuff like CMAP) that I can send you if you like. But if the system is simple enough, one can easily generate the PSF in CHARMM, CHARMM-GUI, VMD, etc.
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>> jalemkul at vt.edu | (540) 231-3129
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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