[gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 71
vijayakumar gosu
vijayakumargosu at gmail.com
Thu Aug 23 15:13:37 CEST 2018
Dear Justin,
Thank you for your prompt response.
I have one more query that can we use the modified trajectory for rerun
option to recompute interaction energies with less number of frames, since
i have long trajectory as well as large complex.
Vijayakumar Gosu Ph.D
On Thu, Aug 23, 2018 at 9:14 PM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: residue-ligand interaction energy using rerun option in
> mdrun (Justin Lemkul)
> 2. Re: SWM4-NDP Simulation (Justin Lemkul)
> 3. Re: specbonds (Justin Lemkul)
> 4. Re: Residue not found in topology (Amir Zeb)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 23 Aug 2018 08:02:17 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] residue-ligand interaction energy using rerun
> option in mdrun
> Message-ID: <e5280e32-b16c-a760-c489-feb862a153b1 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/23/18 6:34 AM, vijayakumar gosu wrote:
> > Dear gromacs users,
> >
> > I want to calculate the interaction energies of one particular residue
> with
> > RNA using rerun option. however i indexed the residue with RNA. in my mdp
> > file i have given energy groups as a r_100 RNA.
> > i ended up with an error Fatal error:
> > "21510 atoms are not part of any of the T-Coupling groups". in
> T-Coupling i
> > have provided r_100_RNA. I guess the error is because of T-Coupling
> > considers the whole protein rather than one residue, because my protein
> > dimer has 21528 atoms. The residue which i am looking has18 atoms. can
> > anyone suggest me how can I rectify this....
>
> You don't need to change anything about tc-grps to recompute an
> interaction energy. Just specify the groups you want in energygrps and
> leave everything else alone.
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 23 Aug 2018 08:05:01 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] SWM4-NDP Simulation
> Message-ID: <7a968035-aa29-9788-6209-7d8a338eece4 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/23/18 4:38 AM, Julian M?ller wrote:
> > Hello,
> >
> > i'd like to simulate pure water and sodium chloride solutions using
> > the drude polarizable SWM4-NDP model. I am new to Gromacs and don't
> > know how to setup the calculation. I simulated SWM4-NDP boxes in
> > LAMMPS before, but LAMMPS lacks the hardwall constraint for the
> > charged particle on a spring.
> >
>
> SWM4-NDP should never have Drudes hitting the hard wall, so for pure
> water, you should never need that algorithm.
>
> > I successfully did small test calculations with the TIP4P water model
> > and want to transfer to the polarizable model from there.
> >
> > In the mailing list I found some hints from 2014, that the preparation
> > of polarizable solvent boxes via pdb2gmx will be available in the near
> > future but no further information on that in the 2018 manual or the
> > help function of pdb2gmx. I also tried to build a SWM4-NDP.itp from
> > the SW.itp but failed miserably at the unfamiliar .itp syntax. Any
> > pointing in the right direction would be greatly appreciated.
> >
>
> GROMACS doesn't yet officially support the extended Lagrangian code, but
> it has supported SCF-based polarization for quite some time. The
> extended Lagrangian that you're likely referring to was coded into
> GROMACS and added to the development repo a few years ago, but
> unfortunately we're still struggling with some domain decomposition
> compatibility issues that I haven't had sufficient time to sort out.
> OpenMP works just fine, but that's obviously going to limit you to small
> systems.
>
> My recommendation at this point is that you use NAMD or OpenMM until we
> can get official support for all the Drude stuff in GROMACS. If you want
> a GROMACS-compatible .itp file for SWM4-NDP, see
> http://mackerell.umaryland.edu/charmm_drude_ff.shtml
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 23 Aug 2018 08:05:29 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] specbonds
> Message-ID: <fa9104e9-9548-3828-1134-3ef4ee544bc7 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 8/23/18 4:09 AM, Momin Ahmad wrote:
> > Hi,
> >
> > i have two different residues and i want a bond defines between them.
> > I know i have to use the specbond.dat file but how do i implement the
> > additional potentials like stretching/angles/dihedrals? Is it enough
> > to just describe them in ffbonded.itp? Example: i have CH3 and NH as
> > different residues and want a bond between C and N. For the topology i
> > want also to define the parameters for the N-H bond, H-C-N/C-N-H angles.
> >
>
> Yes, all bonded parameters go in ffbonded.itp.
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 23 Aug 2018 21:12:20 +0900
> From: Amir Zeb <zebamir85 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Residue not found in topology
> Message-ID:
> <CAF9RtnbbYJ1boqG=U-QhsqKmeMZUO5gxW4a3Y0KCyHmtEu=
> ckA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thanks Justin,
> I have followed what did you suggest for .rtp entry in merged.rtp file of
> charmm36 ff.
> But i could not make .hdb file for ALY. Where can i find the H-information
> for ALY to insert them in merged.hdb file of charmm36 ff?
>
> Amir
>
> On Thu, Aug 23, 2018, 9:02 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 8/23/18 7:52 AM, Bratin Kumar Das wrote:
> > > Hi
> > > You can see that only the problem is coming from hydrogen. So in
> > pdb2gmx
> > > command use -ignh so that it ignores the hydrogen. If you use this this
> > > WARNING will not come.
> >
> > That's not true. The -ignh option ignores H atoms in the input
> > coordinate file and is useful when there are H atoms with names that do
> > not agree with what is specified in the .rtp entry for the given
> > residue. The OP's problem is the opposite: the H are not there but need
> > to be built.
> >
> > -Justin
> >
> > > On Fri, Aug 24, 2018 at 4:00 AM, Amir Zeb <zebamir85 at gmail.com> wrote:
> > >
> > >> Thanks Justin,
> > >>
> > >> Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/
> > and
> > >> generated the parameters for KAC.
> > >> The merged.rtp file was modified by adding the KAC parameters
> > >> That issue fixed, but now I'm getting the following warning which
> > >> ultimately results in fatal error.
> > >>
> > >> WARNING: atom HA is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HA to the hydrogen database of
> > building
> > >> block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HB1 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HB1 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HB2 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HB2 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HG1 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HG1 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HG2 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HG2 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HD1 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HD1 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HD2 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HD2 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HE1 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HE1 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HE2 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HE2 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HZ1 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HI11 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HI11 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HI12 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HI12 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HI13 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HI13 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HZ2 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HZ2 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >>
> > >> WARNING: atom HT2 is missing in residue KAC 33 in the pdb file
> > >> You might need to add atom HT2 to the hydrogen database of
> > >> building block KAC
> > >> in the file merged.hdb (see the manual)
> > >>
> > >> How may I fix this issue?
> > >>
> > >> Thanks in advance!
> > >>
> > >>
> > >> On Wed, Aug 22, 2018 at 4:31 AM Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > >>
> > >>>
> > >>> On 8/22/18 5:26 AM, Bratin Kumar Das wrote:
> > >>>> Hi
> > >>>> In your tool.top file the particular lys molecule residue name
> > you
> > >>> have
> > >>>> to modify. Then it will work..Actually grompp can't find the
> molecule
> > >> in
> > >>>> the topology.
> > >>> The error has nothing to do with grompp. The topology was never
> created
> > >>> because pdb2gmx could not write a topology for KAC.
> > >>>
> > >>> CHARMM36 does support KAC, but not as a standalone residue. In
> CHARMM,
> > >>> one would generate a normal lysine then patch it with the KAC patch.
> To
> > >>> make this work in GROMACS, one would have to create a KAC .rtp entry
> by
> > >>> applying the same logic - modify LYS according to the KAC patch
> (found
> > >>> in the stream/prot/toppar_all36_prot_modify_res.str file from the
> > >>> tarball distributed by Alex MacKerell:
> > >>> http://mackerell.umaryland.edu/charmm_ff.shtml#charmm).
> > >>>
> > >>> -Justin
> > >>>
> > >>>> On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, <
> > >>> 177cy500.bratin at nitk.edu.in>
> > >>>> wrote:
> > >>>>
> > >>>>> Hi
> > >>>>> In your tool.top file the particular lys molecule residue
> name
> > >> you
> > >>>>> have to modify. Then it will work..Actually grompp can't find the
> > >>> molecule
> > >>>>> in the topology.
> > >>>>>
> > >>>>> On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, <zebamir85 at gmail.com>
> wrote:
> > >>>>>
> > >>>>>> Hi gromacs users,
> > >>>>>>
> > >>>>>> I want to simulate a protein where one of the lysine residues is
> > >>> modified
> > >>>>>> to acetylated lysine and has been denoted by KAC. I want to
> simulate
> > >>> it by
> > >>>>>> CharmM 36 ff, but it gave me this error.
> > >>>>>>
> > >>>>>>
> > >>>>>> Program gmx pdb2gmx, VERSION 5.1.4
> > >>>>>> Source code file:
> > >>>>>> /home/chip/Downloads/gromacs-5.1.4/src/gromacs/
> > >> gmxpreprocess/resall.c,
> > >>>>>> line: 645
> > >>>>>>
> > >>>>>> Fatal error:
> > >>>>>> Residue 'KAC' not found in residue topology database
> > >>>>>> For more information and tips for troubleshooting, please check
> the
> > >>>>>> GROMACS
> > >>>>>> website at http://www.gromacs.org/Documentation/Errors
> > >>>>>>
> > >>>>>>
> > >>>>>> Is CharmM 36 ff capable to simulate modified residue acetylated
> > >> lysine?
> > >>>>>> If yes, what is the ff compatible notation for acetylated lysine?
> > >>>>>> If not, which ff can I use to simulate acetylated lysine?
> > >>>>>>
> > >>>>>> Thanks in advance!
> > >>>>>>
> > >>>>>> Amir
> > >>>>>> --
> > >>>>>> Gromacs Users mailing list
> > >>>>>>
> > >>>>>> * Please search the archive at
> > >>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > >>>>>> posting!
> > >>>>>>
> > >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>>>>
> > >>>>>> * For (un)subscribe requests visit
> > >>>>>>
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > >> or
> > >>>>>> send a mail to gmx-users-request at gromacs.org.
> > >>>>>>
> > >>> --
> > >>> ==================================================
> > >>>
> > >>> 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
> > >>> http://www.thelemkullab.com
> > >>>
> > >>> ==================================================
> > >>>
> > >>> --
> > >>> Gromacs Users mailing list
> > >>>
> > >>> * Please search the archive at
> > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >>> posting!
> > >>>
> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>>
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> > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > >>> send a mail to gmx-users-request at gromacs.org.
> > >>>
> > >> --
> > >> Gromacs Users mailing list
> > >>
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> > >>
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> > >> send a mail to gmx-users-request at gromacs.org.
> > >>
> >
> > --
> > ==================================================
> >
> > 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
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
>
>
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