[gmx-users] minimization is not converging (Bratin Kumar Das)

ABEL Stephane Stephane.ABEL at cea.fr
Thu Sep 6 20:29:00 CEST 2018 

>> getting failed for my system

Not clear to me. What are the errors? Did you passed all the steps. CHARMM-ui is quite robust. So if the initial structure of the protein and the pdb correctly formated and complete, CHARMM-GUI should work. 

Stéphane

-----------------------------------------------------------------------------------------
Dear ABEL,
                   I tried CHARMM-gui but the charmm gui is getting failed
for my system.


On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane <Stephane.ABEL at cea.fr> wrote:

> Hi
>
> Did you try to use CHARMM-gui and use the gromacs files generated for this
> system to see if your problem is resolved?
>
> St?phane
>
> ------------------------------
>
> Message: 5
> Date: Thu, 6 Sep 2018 19:55:07 +0530
> From: Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] minimization is not converging
> Message-ID:
>         <CAM7TW5vtko_7pev_5mTEHT4_WX9ps82Vaw+0=A6HjAtAg5xamw@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you sir
>
> On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 9/6/18 10:09 AM, Bratin Kumar Das wrote:
> > > Respected Dr. Justin
> > >                                       To avoid the complicacy I
> solvated
> > > only the protein pdb in a pbc box and tried for minimizatin. There also
> > > minimization is not converging. Sir, till now I learned to carry out
> > > protein ligand system md simulation successfully. I tried all possible
> > ways
> > > to simulate the my membrane protein system. I failed. Is it possible
> that
> > > the PDB file itself have some serious issue with its coordinates. the
> > > structure refinement is required may be.
> >
> > It may, and I have already suggested a few things for you to check.
> > Please do so.
> >
> > If you can provide more specific diagnostics of what is happening,
> > someone on this list might be able to suggest something. What you've
> > provided thus far is a generic instability that no one can diagnose.
> > Investigate the structure, check for pdb2gmx warnings, follow the
> > diagnostics I've already suggested, and report back with specific
> > observations, a PDB code, and exact errors or warnings you get from any
> > program if you need further help.
> >
> > -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
> >
> > ==================================================
> >
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> >
>
>
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------------------------------

Message: 4
Date: Thu, 6 Sep 2018 22:42:01 +0530
From: Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
To: gmx-users at gromacs.org
Cc: "gromacs.org_gmx-users at maillist.sys.kth.se"
        <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] minimization is not converging (Bratin Kumar
        Das)
Message-ID:
        <CAM7TW5srKyNuQfKxEnhJX+LLueZXa9MjGoKMb+YRRWnorxF0MQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Dear ABEL,
                   I tried CHARMM-gui but the charmm gui is getting failed
for my system.


On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane <Stephane.ABEL at cea.fr> wrote:

> Hi
>
> Did you try to use CHARMM-gui and use the gromacs files generated for this
> system to see if your problem is resolved?
>
> St?phane
>
> ------------------------------
>
> Message: 5
> Date: Thu, 6 Sep 2018 19:55:07 +0530
> From: Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] minimization is not converging
> Message-ID:
>         <CAM7TW5vtko_7pev_5mTEHT4_WX9ps82Vaw+0=A6HjAtAg5xamw@
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you sir
>
> On Thu, Sep 6, 2018, 7:52 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 9/6/18 10:09 AM, Bratin Kumar Das wrote:
> > > Respected Dr. Justin
> > >                                       To avoid the complicacy I
> solvated
> > > only the protein pdb in a pbc box and tried for minimizatin. There also
> > > minimization is not converging. Sir, till now I learned to carry out
> > > protein ligand system md simulation successfully. I tried all possible
> > ways
> > > to simulate the my membrane protein system. I failed. Is it possible
> that
> > > the PDB file itself have some serious issue with its coordinates. the
> > > structure refinement is required may be.
> >
> > It may, and I have already suggested a few things for you to check.
> > Please do so.
> >
> > If you can provide more specific diagnostics of what is happening,
> > someone on this list might be able to suggest something. What you've
> > provided thus far is a generic instability that no one can diagnose.
> > Investigate the structure, check for pdb2gmx warnings, follow the
> > diagnostics I've already suggested, and report back with specific
> > observations, a PDB code, and exact errors or warnings you get from any
> > program if you need further help.
> >
> > -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
> >
> > ==================================================
> >
> > --
> > 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.
> >
>
>
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------------------------------

Message: 5
Date: Thu, 6 Sep 2018 13:42:15 -0400
From: Alex <alexanderwien2k at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Fwd: Adding new atom types
Message-ID:
        <CAEDv6u7RP5tORn7SV+V_1NfH5s2JYwQ2Ym-4AWStMaxLmYVdVQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi Tom,
Thanks for the informative response.

For the Gromos FF the gen-pairs is "no" and then the 1-4 interactions are
taken from the parameters existed [ pairtypes ], if I change the gen-pairs
to "yes" in Gromos FF, would you please confirm me that the parameters in [
pairtypes ] is still in privilege for those interactions whose parameters
EXIST in the [ pairtypes ]? And if the parameters are not there they will
be calculated by the fudgeLJ.

Regards,
Alex

On Thu, Sep 6, 2018 at 10:58 AM Thomas Piggot <t.piggot at soton.ac.uk> wrote:

> The GROMOS force fields are somewhat different to the others in that
> they provide specific 1-4 interactions by having several different C12
> parameters for one atomtype (in some cases). The C12 value used depends
> upon the atomtypes involved in the interactions (see tables 7 and 8 of
> https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20090 for more
> information for GROMOS 53A6). This means you cannot directly calculate
> the pairtypes from the nonbonded_params sections of the itp as you do
> not know what C12 value to use for the interaction.
>
> This also needs to be appropriately taken into account when adding a new
> atom type. You also need to explicitly add in the pairtypes, as by
> having multiple potential C12 parameters means it isn't possible to
> generate the pairtypes automatically.
>
> Cheers
>
> Tom
>
> On 06/09/18 15:27, Alex wrote:
> > Dear all,
> >
> > Any idea please about my both questions below?
> > The c6 in both [ nonbond_params ] to [ pairtypes ] comes from the
> > combination rule of c6ij = (c6ii + c6jj)/2 but I could not find any rule
> > about c12 in either sections!
> >
> > Thanks.
> > Alex
> >
> >
> > ---------- Forwarded message ---------
> > From: Alex <alexanderwien2k at gmail.com>
> > Date: Tue, Sep 4, 2018 at 2:43 PM
> > Subject: Adding new atom types
> > To: <gmx-users at gromacs.org>
> >
> >
> > Hi all,
> > Two questions on which your comments would be highly appreciated;
> >
> > 1. What is the difference between [ nonbond_params ] and [ pairtypes ]
> > sections in ffnonbonded.itp file?
> > For Gromos54a7 force filed with the "fudgeLJ = 1", I expected to have
> > similar numbers for an the similar interactions when it is counted as
> > [ nonbond_params
> > ] or as [ pairtypes ] because of the scale = 1, but the "OE OA"
> interaction
> > parameters change in  [ nonbond_params ] to [ pairtypes ], similar story
> > for the " OA O" interaction. Which is in contrast with my
> > understanding of "fudgeLJ
> > = 1".
> >
> >   [ nonbond_params ]
> > ;       i       j       func    c6              c12
> >
> > *        OE      OA      1       2.261954E-03    1.505529E-06*
> > *        OA      O       1       2.261954E-03    1.386510E-06*
> >
> > [ pairtypes ]
> > ;       i       j       func    c6              c12
> > *        OE      OA      1       2.261954E-03    1.265625E-06*
> > *        OA      O       1       2.261954E-03    9.687375E-07*
> >
> > 2. The gmx grompp gives some errors like;
> > ERROR 1 [file topol.top, line xxxx]
> >   No default LJ-14 types
> >
> > Which needs me to introduce new atom type ( of the problematic atoms)
> > in atomtypes.atp
> > and then in ffnonbonded.itp;
> > Would you please confirm the procedure I should take to do so;
> > First I have to add the atom type in atomtypes.atp: OC24 is an example;
> >
> > *echo "OC24 15.99940" >> atomtypes.atp*
> >
> > Then:
> > *Adding "OC24    8       15.99940        0.000000        A
> >        0.0035644156892674973      6.222504156102231e-06" to
> > the ffnonbonded.itp/[ atomtypes ]*
> >
> > Then:
> > *Adding the ";       i       j       func    c6      c12" for the OC24
> > in ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ]*
> >
> > Do I really need to edit the ffnonbonded.itp/[ nonbond_params ] and
> > ffnonbonded.itp/[ pairtypes ] for the interactions of the new atom? or
> the [
> > nonbond_params ] and [ pairtypes ] can be descided/governed by normal
> > combination rule used in the FF, so that I do not need to put them in [
> > nonbond_params ] and ffnonbonded.itp/[ pairtypes ]
> >
> > Thanks.
> > Alex
>
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
>
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