[gmx-users] (no subject)
Navneet Kumar Singh
navneetcdl at gmail.com
Mon Aug 26 20:50:23 CEST 2019
I have seen this in Gromacs manual.
____________________________________________________________________________________
[ virtual_sites2 ]
; Site from funct a
5 1 2 1 0.7439756
for type 3 like this:
[ virtual_sites3 ]
; Site from funct a b
5 1 2 3 1 0.7439756 0.128012
for type 3fd like this:
[ virtual_sites3 ]
; Site from funct a d
5 1 2 3 2 0.5 -0.105
for type 3fad like this:
[ virtual_sites3 ]
; Site from funct theta d
5 1 2 3 3 120 0.5
for type 3out like this:
[ virtual_sites3 ]
; Site from funct a b c
5 1 2 3 4 -0.4 -0.4 6.9281
for type 4fdn like this:
[ virtual_sites4 ]
; Site from funct a b c
5 1 2 3 4 2 1.0 0.9 0.105
______________________________________________________________________________________________________
I have this from unk.itp file.
____________________________________________
[ virtual_sites3 ]
; Site from funct a d
52 1 23 23 2 0 -0.164
[ exclusions ]
; ai aj
1 52 1
52 23 1
52 21 1
52 22 1
52 18 1
52 19 1
52 51 1
52 50 1
____________________________________________
Now I have to add this in topology file. Is this supposed to add in
system.top ?
On Tue, Aug 27, 2019 at 12:11 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/26/19 2:33 PM, Navneet Kumar Singh wrote:
> > I can't understand meaning of this "For all other GROMACS versions, you
> > will have to manually edit the topology to use "3fad" construction and
> > appropriate atom numbers." If I am using version other than the
> > Gromacs2016.x.
> >
> > Can I get example of any topology file where these kind of
> construction've
> > for loan pair done manually in the topology file?
>
> Please see the manual for examples of what the different construction
> types are.
>
> -Justin
>
> > On Mon, Aug 26, 2019 at 11:57 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 8/26/19 1:14 PM, Navneet Kumar Singh wrote:
> >>> Do I have to add vsite3 information from unk.itp to system.top files?
> >> That directive belongs in the topology to which it corresponds. If it is
> >> in unk.itp, then it is already in system.top. You don't need to include
> >> anything else.
> >>
> >> -Justin
> >>
> >>> -maxwarn 1 flag I checked in gromacs 16 version and it's running there.
> >>>
> >>> On Mon, 26 Aug 2019, 00:58 Justin Lemkul, <jalemkul at vt.edu> wrote:
> >>>
> >>>> On 8/25/19 2:17 PM, Navneet Kumar Singh wrote:
> >>>>> Yeah! I have read that.
> >>>>>
> >>>>> uses -maxwarn 1 to produce .tpr file using grompp command as
> mentioned
> >> in
> >>>> Since you are getting an error rather than a warning, that means you
> are
> >>>> not using GROMACS 2016.x, as the instructions I pointed to you say.
> >>>>
> >>>> If you want to use a different GROMACS version, you have to change the
> >>>> topology. Again see the link I provided for a description of what to
> do.
> >>>>
> >>>> -Justin
> >>>>
> >>>>> python script cgenff_charmm2gmx_py2.py
> >>>>>
> >>>>> output of cgenff_charmm2gmx_py2.py
> >>>>>
> >>
> _____________________________________________________________________________________________________________________________________________________________
> >>>>> NOTE 1: Code tested with python 2.7.12. Your version: 2.7.16
> (default,
> >>>> Mar
> >>>>> 26 2019, 10:00:46)
> >>>>> [GCC 5.4.0 20160609]
> >>>>>
> >>>>> NOTE 2: Please be sure to use the same version of CGenFF in your
> >>>>> simulations that was used during parameter generation:
> >>>>> --Version of CGenFF detected in unk.str : 4.0
> >>>>> --Version of CGenFF detected in charmm36-jul2017.ff/forcefield.doc :
> >> 4.0
> >>>>> NOTE 3: To avoid duplicated parameters, do NOT select the 'Include
> >>>>> parameters that are already in CGenFF' option when uploading a
> molecule
> >>>>> into CGenFF.
> >>>>>
> >>>>> NOTE 4: 1 lone pairs found in topology that are not in the mol2 file.
> >>>> This
> >>>>> is not a problem, just FYI!
> >>>>>
> >>>>> ============ DONE ============
> >>>>> Conversion complete.
> >>>>> The molecule topology has been written to unk.itp
> >>>>> Additional parameters needed by the molecule are written to unk.prm,
> >>>> which
> >>>>> needs to be included in the system .top
> >>>>>
> >>>>> PLEASE NOTE: lone pair construction requires duplicate host atom
> >> numbers,
> >>>>> which will make grompp complain
> >>>>> To produce .tpr files, the user MUST use -maxwarn 1 to circumvent
> this
> >>>> check
> >>>>
> >>
> ________________________________________________________________________________________________________________________________________________________________
> >>>>> After that I am using same -maxwarn 1 but still, it's giving error.
> It
> >>>> may
> >>>>> be some silly mistake please let me know.
> >>>>>
> >>>>>
> >>>>> On Sun, Aug 25, 2019 at 9:43 PM Justin Lemkul <jalemkul at vt.edu>
> wrote:
> >>>>>
> >>>>>> On 8/25/19 11:49 AM, Navneet Kumar Singh wrote:
> >>>>>>> Thank You Sir!
> >>>>>>>
> >>>>>>> Attached file can be downloaded from following link.
> >>>>>>>
> >>>>>>> https://fil.email/OR7Nsh0f
> >>>>>>> <https://fil.email/OR7Nsh0f?&showconfirmation=true>
> >>>>>>>
> ____________________________________________________________________
> >>>>>>> Error
> >>>>>>>
> >>>>>>> ERROR 1 [file unk.itp, line 497]:
> >>>>>>> Duplicate atom index (23) in virtual_sites3
> >>>>>>> ___________________________________________________________________
> >>>>>>>
> >>>>>>> It support lone pair construction for halogens only. Please suggest
> >>>> some
> >>>>>>> alternatives.
> >>>>>> The link I provided before describes what you need to do. Please
> >> consult
> >>>>>> that information.
> >>>>>>
> >>>>>> -Justin
> >>>>>>
> >>>>>> --
> >>>>>> ==================================================
> >>>>>>
> >>>>>> Justin A. Lemkul, Ph.D.
> >>>>>> Assistant Professor
> >>>>>> Office: 301 Fralin Hall
> >>>>>> Lab: 303 Engel Hall
> >>>>>>
> >>>>>> Virginia Tech Department of Biochemistry
> >>>>>> 340 West Campus Dr.
> >>>>>> Blacksburg, VA 24061
> >>>>>>
> >>>>>> jalemkul at vt.edu | (540) 231-3129
> >>>>>> http://www.thelemkullab.com
> >>>>>>
> >>>>>> ==================================================
> >>>>>>
> >>>>>> --
> >>>>>> Gromacs Users mailing list
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> >>>>>>
> >>>> --
> >>>> ==================================================
> >>>>
> >>>> Justin A. Lemkul, Ph.D.
> >>>> Assistant Professor
> >>>> Office: 301 Fralin Hall
> >>>> Lab: 303 Engel Hall
> >>>>
> >>>> Virginia Tech Department of Biochemistry
> >>>> 340 West Campus Dr.
> >>>> Blacksburg, VA 24061
> >>>>
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> >>>> http://www.thelemkullab.com
> >>>>
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> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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> >> Gromacs Users mailing list
> >>
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> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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>
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--
Thanks & Regards
_______________________________________________________
[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647 <+918017967647> |
E navneetcdl at gmail.com <navneetcdl at gmail.com>
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
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