[gmx-users] xpm2ps
Hello everyone When I use xpm2ps in Gromacs 2018.3 and open .eps file, I see that a balck line cover the numbers in y and x axis. Any person can help me?! -- 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.
[gmx-users] Add residue to force field
Hello. For my MD I need a GTP residue. So I made it by modifying ATP residue in gromos 54A7 force field by guanosine base. First time I save it in GTP.rtp and my energy minimisation steps was 30,000 steps because of one atom in GTP. In next try I add GTP residue in aminoaciduria.rtp which contains all amino acids even ATP residue. My energy minimisation steps was about 3,000 steps because of one atom in my ligand! Why this happened?! -- 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.
Re: [gmx-users] Topology file
thanks Justin for your helps. the pdb2gmx make posre_chain_A.itp but don't write any thing about it in my topol.top!!! Can I add it in my topol.top file?! And what's its template for it?! On Fri, 5 Oct 2018 17:08 Justin Lemkul, wrote: > > > On 10/4/18 6:53 PM, Mahdi Sobati Nezhad wrote: > > Hello Gromacs users. > > When I use pdb2gmx the Gromacs make pores.itp but in my topol.top there > is > > no any porse.itp > > What can I do?! > > Do it's important that porse.itp should be in topol.top or its enough > that > > pdb2gmx make porse.itp?! > > pdb2gmx writes the restraint file by default and it is a non-optional > output. If you didn't get a posre.itp file, there should be glaringly > obvious error messages as to why pdb2gmx failed. If pdb2gmx completed > normally, you must have a restraint file. It may be named something > different (like posre_Chain_A.itp or something) if you have chain > identifiers in your input coordinate file. > > -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 > > == > > -- > 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.
Re: [gmx-users] Topology file
Thanks rose for your help. so for ligand and protein interaction its better that I use position restraints On Wed, 10 Oct 2018 17:07 rose rahmani, wrote: > First, i think it's better to ask WHY > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > That's why people use position restraints. > > About WHEN, sometimes your molecule behavior is different in > box. For instance you study the interaction of your molecule with surface. > So the molecule need to be free and move in a box to find its best > configuration toward surface. Because its properties may differ in > different part of box. You can't put a restriction on it, because it's > distance and configuration, is crucial in interacting with surface... > Maybe it's not a scientific explanation of an issue( as justin masterly do) > but i just tried to share my experience. Hope it helps! > > Best > > Rose > > > > On Wed, 10 Oct 2018, 16:21 Mahdi Sobati Nezhad, < > mahdisobatinez...@gmail.com> > wrote: > > > Thanks rose. Can you tell me more about which cases I should use position > > restrictions?! > > Thanks > > > > On Fri, 5 Oct 2018 10:33 rose rahmani, wrote: > > > > > Hi, > > > > > > It depends on you, wheter you want to put position restriction on your > > > molecule you should add posre.itp to topol.top or not. > > > But whenever you use define=-DPOSRES in your .mdp file, GROMACS can > read > > > posre.itp files in topol.top an apply position restriction to molecule. > > > > > > Rose > > > > > > On Fri, 5 Oct 2018, 02:24 Mahdi Sobati Nezhad, < > > > mahdisobatinez...@gmail.com> > > > wrote: > > > > > > > Hello Gromacs users. > > > > When I use pdb2gmx the Gromacs make pores.itp but in my topol.top > there > > > is > > > > no any porse.itp > > > > What can I do?! > > > > Do it's important that porse.itp should be in topol.top or its enough > > > that > > > > pdb2gmx make porse.itp?! > > > > > > > > Thanks > > > > -- > > > > 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. > > > > > -- > > 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. > -- 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.
Re: [gmx-users] Topology file
Thanks rose. Can you tell me more about which cases I should use position restrictions?! Thanks On Fri, 5 Oct 2018 10:33 rose rahmani, wrote: > Hi, > > It depends on you, wheter you want to put position restriction on your > molecule you should add posre.itp to topol.top or not. > But whenever you use define=-DPOSRES in your .mdp file, GROMACS can read > posre.itp files in topol.top an apply position restriction to molecule. > > Rose > > On Fri, 5 Oct 2018, 02:24 Mahdi Sobati Nezhad, < > mahdisobatinez...@gmail.com> > wrote: > > > Hello Gromacs users. > > When I use pdb2gmx the Gromacs make pores.itp but in my topol.top there > is > > no any porse.itp > > What can I do?! > > Do it's important that porse.itp should be in topol.top or its enough > that > > pdb2gmx make porse.itp?! > > > > Thanks > > -- > > 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. > -- 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.
[gmx-users] Topology file
Hello Gromacs users. When I use pdb2gmx the Gromacs make pores.itp but in my topol.top there is no any porse.itp What can I do?! Do it's important that porse.itp should be in topol.top or its enough that pdb2gmx make porse.itp?! Thanks -- 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.
[gmx-users] Change in atom name
Hello Gromacs users. My ligand have two 'Cl' atoms. I cut atoms from ligand.gro and paste it in complex.gro and then open complex.gro in VMD and I see that the VMD shows my atoms as Carbon!!! Do this will not have any effect in my MD?! Thanks -- 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.
[gmx-users] Topology file.
Hello everyone I use Gromacs 18.3. when I use the command "gmx pdb2gmx -f protein.pdb -o protein.gro" it makes a topology file. But this topology haven't "posre_Chain _A.itp" or any other posre in part "; Include chain topologies" im confused, that what is wrong?! Do I can add this posre parts into topology.top?! Or any other idea?! -- 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.
Re: [gmx-users] HB3 ATOM
please excuse me sir On Mon, 3 Sep 2018 22:59 Justin Lemkul, wrote: > > > On 9/3/18 2:28 PM, Mahdi Sobati Nezhad wrote: > > how can I build hydrogens own, after -ignh command?! > > Please re-read what I just said. > > -Justin > > > On Mon, 3 Sep 2018 22:55 Justin Lemkul, wrote: > > > >> > >> On 9/3/18 2:24 PM, Mahdi Sobati Nezhad wrote: > >>> Yes. Now my problem is HG in residue CYS that I don't know rename to > >> what!!! > >> > >> Either the names in the PDB file need to be made consistent with what is > >> in the .rtp file, or you should use -ignh to have pdb2gmx ignore all > >> input H atoms and build its own, all of which will be properly named. > >> > >> -Justin > >> > >>> On Mon, 3 Sep 2018 22:49 Justin Lemkul, wrote: > >>> > >>>> On 9/3/18 6:27 AM, Mahdi Sobati Nezhad wrote: > >>>>> Hi > >>>>> my pdb file named HB2 and HB3 but .rtp file in my force field named > >>>> HB1and > >>>>> HB2. and so on error "atom HB3 in residue xxx was not found in rtp > >> entry" > >>>>> can I rename HB2 to HB1 and HB3 to HB2 ? > >>>>> or any idea?! > >>>> Have you tried it? > >>>> > >>>> -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 > >>>> > >>>> == > >>>> > >>>> -- > >>>> 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. > >> > > -- > == > > 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.
Re: [gmx-users] HB3 ATOM
how can I build hydrogens own, after -ignh command?! On Mon, 3 Sep 2018 22:55 Justin Lemkul, wrote: > > > On 9/3/18 2:24 PM, Mahdi Sobati Nezhad wrote: > > Yes. Now my problem is HG in residue CYS that I don't know rename to > what!!! > > Either the names in the PDB file need to be made consistent with what is > in the .rtp file, or you should use -ignh to have pdb2gmx ignore all > input H atoms and build its own, all of which will be properly named. > > -Justin > > > On Mon, 3 Sep 2018 22:49 Justin Lemkul, wrote: > > > >> > >> On 9/3/18 6:27 AM, Mahdi Sobati Nezhad wrote: > >>> Hi > >>> my pdb file named HB2 and HB3 but .rtp file in my force field named > >> HB1and > >>> HB2. and so on error "atom HB3 in residue xxx was not found in rtp > entry" > >>> can I rename HB2 to HB1 and HB3 to HB2 ? > >>> or any idea?! > >> Have you tried it? > >> > >> -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 > >> > >> == > >> > >> -- > >> 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.
Re: [gmx-users] HB3 ATOM
Yes. Now my problem is HG in residue CYS that I don't know rename to what!!! On Mon, 3 Sep 2018 22:49 Justin Lemkul, wrote: > > > On 9/3/18 6:27 AM, Mahdi Sobati Nezhad wrote: > > Hi > > my pdb file named HB2 and HB3 but .rtp file in my force field named > HB1and > > HB2. and so on error "atom HB3 in residue xxx was not found in rtp entry" > > can I rename HB2 to HB1 and HB3 to HB2 ? > > or any idea?! > Have you tried it? > > -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 > > == > > -- > 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.
[gmx-users] HB3 ATOM
Hi my pdb file named HB2 and HB3 but .rtp file in my force field named HB1and HB2. and so on error "atom HB3 in residue xxx was not found in rtp entry" can I rename HB2 to HB1 and HB3 to HB2 ? or any idea?! -- 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.
Re: [gmx-users] Getting ligand's topology
can I use SWISSPARAM or MATCH servers?! On Wed, 22 Aug 2018 23:50 Justin Lemkul, wrote: > > > On 8/22/18 3:18 PM, Mahdi Sobati Nezhad wrote: > > Thanks, do acpype is for charmm?! > > > No, it is for AMBER. > > -Justin > > > On Wed, 22 Aug 2018 09:43 Bratin Kumar Das, <177cy500.bra...@nitk.edu.in > > > > wrote: > > > >> Hi > >> You can use acpype for generating the ligand topology. It's simple > and > >> easy > >> > >> On Mon, Aug 20, 2018 at 5:03 PM, Justin Lemkul wrote: > >> > >>> > >>> On 8/20/18 2:40 AM, Mahdi Sobati Nezhad wrote: > >>> > >>>> thanks for your taking time. and so on for a begginer like me there is > >> no > >>>> any way > >>>> > >>> Well, there is if you're willing to invest the time in learning some > >>> challenging concepts and some new software. But no one should expect > that > >>> for any given ligand, there is a perfect tool for magically giving you > a > >>> perfect topology. That's rarely the case. > >>> > >>> -Justin > >>> > >>> > >>> On Mon, 20 Aug 2018 00:29 Justin Lemkul, wrote: > >>>> > >>>>> On 8/19/18 10:20 AM, RAHUL SURESH wrote: > >>>>> > >>>>>> Hi. > >>>>>> > >>>>>> First, I feel grimaces users may not entertain other discussions in > >>>>>> > >>>>> grimace > >>>>> > >>>>>> forum. You can directly mail me if it’s something apart from > gromacs. > >>>>>> > >>>>>> Then, I am not sure about other servers. > >>>>>> > >>>>>> Looking at your str file, I would say that it definitely need some > >> work > >>>>> on > >>>>> > >>>>>> our molecule. As I said before try zinc database. > >>>>>> > >>>>> I don't see how the ZINC database is relevant. Either the .mol2 > >>>>> submitted to the CGenFF server is valid or it is not. > >>>>> > >>>>> CGenFF is nice in that it tells you the potential problems with the > >>>>> ligand topology. AFAIK, no other servers do. You get a "black box" > >>>>> output that you're supposed to trust. The areas pinpointed by CGenFF > >>>>> should be examined carefully. The parameters may actually be fine, > but > >>>>> the penalties are there to tell the user when there is a functional > >>>>> group that is not well described by existing molecules in the CGenFF > >>>>> database, from which the analogies are made. > >>>>> > >>>>> There is a CGenFF tutorial available online that walks a user through > >>>>> the whole process. It requires subdividing a molecule into units that > >>>>> can be parametrized easily; large molecules should always be broken > >> down > >>>>> into manageable pieces that have all the necessary degrees of > freedom. > >>>>> > >>>>> The tutorial materials can be accessed here: > >>>>> http://mackerell.umaryland.edu/~kenno/cgenff/download.php > >>>>> > >>>>> CHARMM/CGenFF parametrization assumes some familiarity with QM > >>>>> calculations (geometry optimizations, potential energy scans, > >>>>> interaction energies) but the methodology is published in great > detail, > >>>>> and the CGenFF paper itself is a worked example of how to > parametrize a > >>>>> molecule. While the developers have made every effort to make the > >>>>> methodology publicly available, ligand parametrization and refinement > >> is > >>>>> still an advanced concept that is best suited for experienced users, > as > >>>>> knowledge of fundamental principles of MD, QM, and empirical energy > >>>>> functions is required. > >>>>> > >>>>> -Justin > >>>>> > >>>>> Thank you > >>>>>> > >>>>>> On Sun, 19 Aug 2018 at 1:37 PM, Mahdi Sobati Nezhad < > >>>>>> mahdisobatinez...@gmail.com> wrote: > >>>>>> > >>>>>> thanks. > >>>>>>> if I use MATCH ser
Re: [gmx-users] Getting ligand's topology
Thanks, do acpype is for charmm?! On Wed, 22 Aug 2018 09:43 Bratin Kumar Das, <177cy500.bra...@nitk.edu.in> wrote: > Hi >You can use acpype for generating the ligand topology. It's simple and > easy > > On Mon, Aug 20, 2018 at 5:03 PM, Justin Lemkul wrote: > > > > > > > On 8/20/18 2:40 AM, Mahdi Sobati Nezhad wrote: > > > >> thanks for your taking time. and so on for a begginer like me there is > no > >> any way > >> > > > > Well, there is if you're willing to invest the time in learning some > > challenging concepts and some new software. But no one should expect that > > for any given ligand, there is a perfect tool for magically giving you a > > perfect topology. That's rarely the case. > > > > -Justin > > > > > > On Mon, 20 Aug 2018 00:29 Justin Lemkul, wrote: > >> > >> > >>> On 8/19/18 10:20 AM, RAHUL SURESH wrote: > >>> > >>>> Hi. > >>>> > >>>> First, I feel grimaces users may not entertain other discussions in > >>>> > >>> grimace > >>> > >>>> forum. You can directly mail me if it’s something apart from gromacs. > >>>> > >>>> Then, I am not sure about other servers. > >>>> > >>>> Looking at your str file, I would say that it definitely need some > work > >>>> > >>> on > >>> > >>>> our molecule. As I said before try zinc database. > >>>> > >>> I don't see how the ZINC database is relevant. Either the .mol2 > >>> submitted to the CGenFF server is valid or it is not. > >>> > >>> CGenFF is nice in that it tells you the potential problems with the > >>> ligand topology. AFAIK, no other servers do. You get a "black box" > >>> output that you're supposed to trust. The areas pinpointed by CGenFF > >>> should be examined carefully. The parameters may actually be fine, but > >>> the penalties are there to tell the user when there is a functional > >>> group that is not well described by existing molecules in the CGenFF > >>> database, from which the analogies are made. > >>> > >>> There is a CGenFF tutorial available online that walks a user through > >>> the whole process. It requires subdividing a molecule into units that > >>> can be parametrized easily; large molecules should always be broken > down > >>> into manageable pieces that have all the necessary degrees of freedom. > >>> > >>> The tutorial materials can be accessed here: > >>> http://mackerell.umaryland.edu/~kenno/cgenff/download.php > >>> > >>> CHARMM/CGenFF parametrization assumes some familiarity with QM > >>> calculations (geometry optimizations, potential energy scans, > >>> interaction energies) but the methodology is published in great detail, > >>> and the CGenFF paper itself is a worked example of how to parametrize a > >>> molecule. While the developers have made every effort to make the > >>> methodology publicly available, ligand parametrization and refinement > is > >>> still an advanced concept that is best suited for experienced users, as > >>> knowledge of fundamental principles of MD, QM, and empirical energy > >>> functions is required. > >>> > >>> -Justin > >>> > >>> Thank you > >>>> > >>>> > >>>> On Sun, 19 Aug 2018 at 1:37 PM, Mahdi Sobati Nezhad < > >>>> mahdisobatinez...@gmail.com> wrote: > >>>> > >>>> thanks. > >>>>> if I use MATCH server or swissparam, I can trust to their results?! > >>>>> > >>>>> And this is my error when I use CGenFF: > >>>>> "readmol2 warning: non-unique atoms were renamed. Now processing > >>>>> > >>>> molecule > >>> > >>>> mae ..." > >>>>> > >>>>> And this is my output of penalty: > >>>>> > >>>>> * Toppar stream file generated by * CHARMM General Force Field > (CGenFF) > >>>>> program version 2.2.0 * For use with CGenFF version 4.0 * read rtf > card > >>>>> append * Topologies generated by * CHARMM General Force Field > (CGenFF) > >>>>> program version 2.2.0 * 36 1 ! "penalty" is the highest penalty score > >>
Re: [gmx-users] Getting ligand's topology
thanks for your taking time. and so on for a begginer like me there is no any way On Mon, 20 Aug 2018 00:29 Justin Lemkul, wrote: > > > On 8/19/18 10:20 AM, RAHUL SURESH wrote: > > Hi. > > > > First, I feel grimaces users may not entertain other discussions in > grimace > > forum. You can directly mail me if it’s something apart from gromacs. > > > > Then, I am not sure about other servers. > > > > Looking at your str file, I would say that it definitely need some work > on > > our molecule. As I said before try zinc database. > > I don't see how the ZINC database is relevant. Either the .mol2 > submitted to the CGenFF server is valid or it is not. > > CGenFF is nice in that it tells you the potential problems with the > ligand topology. AFAIK, no other servers do. You get a "black box" > output that you're supposed to trust. The areas pinpointed by CGenFF > should be examined carefully. The parameters may actually be fine, but > the penalties are there to tell the user when there is a functional > group that is not well described by existing molecules in the CGenFF > database, from which the analogies are made. > > There is a CGenFF tutorial available online that walks a user through > the whole process. It requires subdividing a molecule into units that > can be parametrized easily; large molecules should always be broken down > into manageable pieces that have all the necessary degrees of freedom. > > The tutorial materials can be accessed here: > http://mackerell.umaryland.edu/~kenno/cgenff/download.php > > CHARMM/CGenFF parametrization assumes some familiarity with QM > calculations (geometry optimizations, potential energy scans, > interaction energies) but the methodology is published in great detail, > and the CGenFF paper itself is a worked example of how to parametrize a > molecule. While the developers have made every effort to make the > methodology publicly available, ligand parametrization and refinement is > still an advanced concept that is best suited for experienced users, as > knowledge of fundamental principles of MD, QM, and empirical energy > functions is required. > > -Justin > > > Thank you > > > > > > On Sun, 19 Aug 2018 at 1:37 PM, Mahdi Sobati Nezhad < > > mahdisobatinez...@gmail.com> wrote: > > > >> thanks. > >> if I use MATCH server or swissparam, I can trust to their results?! > >> > >> And this is my error when I use CGenFF: > >> "readmol2 warning: non-unique atoms were renamed. Now processing > molecule > >> mae ..." > >> > >> And this is my output of penalty: > >> > >> * Toppar stream file generated by * CHARMM General Force Field (CGenFF) > >> program version 2.2.0 * For use with CGenFF version 4.0 * read rtf card > >> append * Topologies generated by * CHARMM General Force Field (CGenFF) > >> program version 2.2.0 * 36 1 ! "penalty" is the highest penalty score of > >> the associated parameters. ! Penalties lower than 10 indicate the > analogy > >> is fair; penalties between 10 ! and 50 mean some basic validation is > >> recommended; penalties higher than ! 50 indicate poor analogy and > mandate > >> extensive validation/optimization. RESI mae 0.000 ! param penalty= > 198.400 > >> ; charge penalty= 142.287 GROUP ! CHARGE CH_PENALTY ATOM C1 CG2R61 > 0.227 ! > >> 0.000 ATOM C2 CG2R61 -0.117 ! 2.688 ATOM C3 CG2R61 -0.003 ! 5.191 ATOM > C4 > >> CG2R61 -0.117 ! 2.688 ATOM C5 CG2R61 0.227 ! 0.000 ATOM C6 CG2R61 0.217 > ! > >> 0.000 ATOM H1 HGR61 0.115 ! 0.000 ATOM H2 HGR61 0.115 ! 0.000 ATOM O1 > OG301 > >> -0.391 ! 0.000 ATOM O2 OG301 -0.391 ! 0.000 ATOM O3 OG301 -0.391 ! 0.000 > >> ATOM C7 CG331 -0.100 ! 0.000 ATOM H3 HGA3 0.090 ! 0.000 ATOM H4 HGA3 > 0.090 > >> ! 0.000 ATOM H5 HGA3 0.090 ! 0.000 ATOM C8 CG331 -0.100 ! 0.000 ATOM H6 > >> HGA3 0.090 ! 0.000 ATOM H7 HGA3 0.090 ! 0.000 ATOM H8 HGA3 0.090 ! 0.000 > >> ATOM C9 CG331 -0.100 ! 0.000 ATOM H9 HGA3 0.090 ! 0.000 ATOM H10 HGA3 > 0.090 > >> ! 0.000 ATOM H11 HGA3 0.090 ! 0.000 ATOM C10 CG3C51 0.317 ! 142.287 > ATOM N1 > >> NG3C51 -0.343 ! 101.066 ATOM C11 CG321 -0.072 ! 70.919 ATOM H12 HGA2 > 0.090 > >> ! 2.500 ATOM H13 HGA2 0.090 ! 2.500 ATOM C12 CG2R53 0.464 ! 90.248 ATOM > N2 > >> NG2R50 -0.515 ! 21.469 ATOM N3 NG3C51 -0.417 ! 87.522 ATOM H14 HGP1 > 0.341 ! > >> 3.424 ATOM C13 CG321 0.028 ! 26.713 ATOM H15 HGA2 0.090 ! 2.659 ATOM N4 > >> NG3N1 -0.689 ! 58.305 ATOM C14 CG2R61 0.140 ! 19.097 ATOM C15 CG2R61 > -0.110 > >> ! 13.488 ATOM C16 CG2R61 0
Re: [gmx-users] Getting ligand's topology
thanks. if I use MATCH server or swissparam, I can trust to their results?! And this is my error when I use CGenFF: "readmol2 warning: non-unique atoms were renamed. Now processing molecule mae ..." And this is my output of penalty: * Toppar stream file generated by * CHARMM General Force Field (CGenFF) program version 2.2.0 * For use with CGenFF version 4.0 * read rtf card append * Topologies generated by * CHARMM General Force Field (CGenFF) program version 2.2.0 * 36 1 ! "penalty" is the highest penalty score of the associated parameters. ! Penalties lower than 10 indicate the analogy is fair; penalties between 10 ! and 50 mean some basic validation is recommended; penalties higher than ! 50 indicate poor analogy and mandate extensive validation/optimization. RESI mae 0.000 ! param penalty= 198.400 ; charge penalty= 142.287 GROUP ! CHARGE CH_PENALTY ATOM C1 CG2R61 0.227 ! 0.000 ATOM C2 CG2R61 -0.117 ! 2.688 ATOM C3 CG2R61 -0.003 ! 5.191 ATOM C4 CG2R61 -0.117 ! 2.688 ATOM C5 CG2R61 0.227 ! 0.000 ATOM C6 CG2R61 0.217 ! 0.000 ATOM H1 HGR61 0.115 ! 0.000 ATOM H2 HGR61 0.115 ! 0.000 ATOM O1 OG301 -0.391 ! 0.000 ATOM O2 OG301 -0.391 ! 0.000 ATOM O3 OG301 -0.391 ! 0.000 ATOM C7 CG331 -0.100 ! 0.000 ATOM H3 HGA3 0.090 ! 0.000 ATOM H4 HGA3 0.090 ! 0.000 ATOM H5 HGA3 0.090 ! 0.000 ATOM C8 CG331 -0.100 ! 0.000 ATOM H6 HGA3 0.090 ! 0.000 ATOM H7 HGA3 0.090 ! 0.000 ATOM H8 HGA3 0.090 ! 0.000 ATOM C9 CG331 -0.100 ! 0.000 ATOM H9 HGA3 0.090 ! 0.000 ATOM H10 HGA3 0.090 ! 0.000 ATOM H11 HGA3 0.090 ! 0.000 ATOM C10 CG3C51 0.317 ! 142.287 ATOM N1 NG3C51 -0.343 ! 101.066 ATOM C11 CG321 -0.072 ! 70.919 ATOM H12 HGA2 0.090 ! 2.500 ATOM H13 HGA2 0.090 ! 2.500 ATOM C12 CG2R53 0.464 ! 90.248 ATOM N2 NG2R50 -0.515 ! 21.469 ATOM N3 NG3C51 -0.417 ! 87.522 ATOM H14 HGP1 0.341 ! 3.424 ATOM C13 CG321 0.028 ! 26.713 ATOM H15 HGA2 0.090 ! 2.659 ATOM N4 NG3N1 -0.689 ! 58.305 ATOM C14 CG2R61 0.140 ! 19.097 ATOM C15 CG2R61 -0.110 ! 13.488 ATOM C16 CG2R61 0.036 ! 13.718 ATOM C17 CG2R61 -0.112 ! 0.000 ATOM H16 HGR61 0.115 ! 0.000 ATOM C18 CG2R61 0.071 ! 0.000 ATOM C19 CG2R61 -0.089 ! 0.000 ATOM H17 HGR61 0.115 ! 0.000 ATOM S SG311 -0.210 ! 105.411 ATOM H18 HGP3 0.160 ! 4.359 ATOM H19 HGR62 0.144 ! 0.000 ATOM Cl1 CLGR1 -0.152 ! 2.500 ATOM Cl2 CLGR1 -0.167 ! 0.000 ATOM HXT1 HGA1 0.090 ! 5.954 ATOM HXT2 HGA2 0.090 ! 2.659 ATOM HN HGP1 0.394 ! 9.368 ATOM LP1 LPH 0.050 ! on Cl1 ATOM LP2 LPH 0.050 ! on Cl2 Thanks for your taking time On Sat, 18 Aug 2018 22:31 RAHUL SURESH, wrote: > I cannot assist you much with the description of your ligand. But what I > have seen is, ring with N shows maximum penalities in most cases. > > When you optimise with mp2, the structure shows no much changes. > So penalty is same most time. > > Try to download file from Zinc15 database which is most preferred file > cgenff. Still the penalty may exist in cse of N in ring. It could be > optimised using ffTK. Again I find your structure is pretty big which will > be time consuming. Or you have to adapt divide and conquer method, which is > going to be complicated. So it’s your wise choice always. Maybe others, > especially Dr. Justin or Dr. Mark could give you a better soln. > > Thank you > > On Sat, 18 Aug 2018 at 10:17 PM, Mahdi Sobati Nezhad < > mahdisobatinez...@gmail.com> wrote: > > > Thanks for your help. > > my ligand is three rings that connects with a carbon and this rings have > > Nitrogen, oxygen, sulfur, carbon and Chlor... > > And high penaltys are just for that ring that contains Nitrogen, carbon > and > > sulfur > > And so on my choice is just using ffTK?! > > > > > > On Sat, 18 Aug 2018 21:05 RAHUL SURESH, wrote: > > > > > Hi. > > > > > > To resolve the penalties are bit complicated. Tools like ffTK can help > > you > > > do it. But output from ffTK is as in charmm and henceforth it take > > > additional work ( was difficult for me ) to modify it to Gromacs > > acceptable > > > format. > > > > > > I personally don’t appreciate this method as it is very time consuming > if > > > your structure is big and having penalties in dihedrals which again > make > > it > > > complicated. > > > Thank you > > > > > > On Sat, 18 Aug 2018 at 7:02 PM, Mahdi Sobati Nezhad < > > > mahdisobatinez...@gmail.com> wrote: > > > > > > > Hi > > > > I'm a begginer in taking ligand's topology from CGENFF and my '.str' > > file > > > > have some high penalty numbers. What I can do?! > > > > And how I can do validation and optimization?! > > > > I read the FAQ in its server but I don't understand!!! > > > > Thanks > > > > -- > > > > Gromacs Users maili
Re: [gmx-users] Getting ligand's topology
Thanks for your help. my ligand is three rings that connects with a carbon and this rings have Nitrogen, oxygen, sulfur, carbon and Chlor... And high penaltys are just for that ring that contains Nitrogen, carbon and sulfur And so on my choice is just using ffTK?! On Sat, 18 Aug 2018 21:05 RAHUL SURESH, wrote: > Hi. > > To resolve the penalties are bit complicated. Tools like ffTK can help you > do it. But output from ffTK is as in charmm and henceforth it take > additional work ( was difficult for me ) to modify it to Gromacs acceptable > format. > > I personally don’t appreciate this method as it is very time consuming if > your structure is big and having penalties in dihedrals which again make it > complicated. > Thank you > > On Sat, 18 Aug 2018 at 7:02 PM, Mahdi Sobati Nezhad < > mahdisobatinez...@gmail.com> wrote: > > > Hi > > I'm a begginer in taking ligand's topology from CGENFF and my '.str' file > > have some high penalty numbers. What I can do?! > > And how I can do validation and optimization?! > > I read the FAQ in its server but I don't understand!!! > > Thanks > > -- > > 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. > > > -- > *Regards,* > *Rahul * > -- > 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.
[gmx-users] Getting ligand's topology
Hi I'm a begginer in taking ligand's topology from CGENFF and my '.str' file have some high penalty numbers. What I can do?! And how I can do validation and optimization?! I read the FAQ in its server but I don't understand!!! Thanks -- 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.
Re: [gmx-users] GTP
Excuse me I don't understand completely, I residue I see Gua and Ade. You say I change Gua base with Ade base in the ATPs residue?! What about my hydrogen bonds?! Do my charges don't change?! Thanks for your help On Wed, 15 Aug 2018 16:00 Justin Lemkul, wrote: > > > On 8/15/18 3:05 AM, Mahdi Sobati Nezhad wrote: > > hello > > I'm working on a protein that contains GTP in its structure. I can't find > > any force field that contains GTP's residue but I find a force field that > > contains the ATPs residue! There is any way that I can convert ATP to > GTP?! > > Or any other idea?! > > Just replace the Ade base with Gua. > > -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 > > == > > -- > 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.
[gmx-users] GTP
hello I'm working on a protein that contains GTP in its structure. I can't find any force field that contains GTP's residue but I find a force field that contains the ATPs residue! There is any way that I can convert ATP to GTP?! Or any other idea?! (I work with gromos 43a1 force field) thanks -- 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.
