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-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > 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 <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] residue-ligand interaction energy using rerun > option in mdrun > Message-ID: <e5280e32-b16c-a760-c489-feb862a15...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 2 > Date: Thu, 23 Aug 2018 08:05:01 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] SWM4-NDP Simulation > Message-ID: <7a968035-aa29-9788-6209-7d8a338ee...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 3 > Date: Thu, 23 Aug 2018 08:05:29 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] specbonds > Message-ID: <fa9104e9-9548-3828-1134-3ef4ee544...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 4 > Date: Thu, 23 Aug 2018 21:12:20 +0900 > From: Amir Zeb <zebami...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Residue not found in topology > Message-ID: > <CAF9RtnbbYJ1boqG=U-QhsqKmeMZUO5gxW4a3Y0KCyHmtEu= > c...@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 <jalem...@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 <zebami...@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 <jalem...@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.bra...@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, <zebami...@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-requ...@gromacs.org. > > >>>>>> > > >>> -- > > >>> ================================================== > > >>> > > >>> Justin A. Lemkul, Ph.D. > > >>> Assistant Professor > > >>> Virginia Tech Department of Biochemistry > > >>> > > >>> 303 Engel Hall > > >>> 340 West Campus Dr. > > >>> Blacksburg, VA 24061 > > >>> > > >>> jalem...@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 > > >>> > > >>> * For (un)subscribe requests visit > > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > >>> send a mail to gmx-users-requ...@gromacs.org. > > >>> > > >> -- > > >> 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-requ...@gromacs.org. > > >> > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Virginia Tech Department of Biochemistry > > > > 303 Engel Hall > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@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 > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > ------------------------------ > > -- > 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-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 172, Issue 71 > ****************************************************** > -- 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-requ...@gromacs.org.