Re: [gmx-users] SPC with amber?

[Rafael I. Silverman y de la Vega]

Ok, thanks, I may just do that


On Tue, Sep 24, 2013 at 2:42 PM, Mark Abraham wrote:

> The FF+water combinations still work the same way they did 3 years
> ago! :-) The important question is whether validation for the
> observables has occurred. (And no relevant problems were seen). If the
> paper does not support its decision to mix and match, go and ask them
> why it was reasonable!
>
> Mark
>
> On Tue, Sep 24, 2013 at 10:58 PM, Rafael I. Silverman y de la Vega
>  wrote:
> > Dear all,
> > I have been trying to evaluate a paper that used amber99 with SPC water
> to
> > simulate a protein. How would this affect the results, is it important? I
> > googled for a bit, all I found was:
> >  "Amber, charmm and OPLS-AA were developed with TIP3P, and that should be
> > the default. Except that charmm uses a TIP3P with lennard-Jones on the
> > waters, and that should probably be the default with charmm.
> >  >B.t.w., how transferable are water models between ff's? I've always
> been
> > thought that >they are actually non-transferable (or at least that is
>  what
> > I remember), making e.g. >Amber/SPCe a bad option, as would
>  gromos/tip4p.?
> >  Nobody really knows."
> >
> > from 2010, have things changed in 3 years, and forcefields work better
> with
> > water models not developed specifically for that ff?
> > Thanks
> > --
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[gmx-users] SPC with amber?

[Rafael I. Silverman y de la Vega]

Dear all,
I have been trying to evaluate a paper that used amber99 with SPC water to
simulate a protein. How would this affect the results, is it important? I
googled for a bit, all I found was:
 "Amber, charmm and OPLS-AA were developed with TIP3P, and that should be
the default. Except that charmm uses a TIP3P with lennard-Jones on the
waters, and that should probably be the default with charmm.
 >B.t.w., how transferable are water models between ff's? I've always been
thought that >they are actually non-transferable (or at least that is  what
I remember), making e.g. >Amber/SPCe a bad option, as would  gromos/tip4p.?
 Nobody really knows."

from 2010, have things changed in 3 years, and forcefields work better with
water models not developed specifically for that ff?
Thanks
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Re: [gmx-users] changing atom types versus adding dihedrals to atom types

[Rafael I. Silverman y de la Vega]

Sulpher is important, but it is in the apoprotein, not the parametrized
prosthetic group


On Thu, Sep 19, 2013 at 6:51 PM, Rafael I. Silverman y de la Vega <
rsilv...@ucsc.edu> wrote:

> Hmm, I will have to do some more controls then, but I  prob dont have time
> to do them till after quals this fall...
> You mention Hartree-Fock methods, does this mean that you disfavor DFT for
> some reason for this purpose?
>
>
> On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote:
>>
>>> Can you give some examples of how these verifications are  different for
>>> different force fields? It doesnt seem like verifying takes that much
>>> time,
>>> but a theorist prof in my department told me not to worry as long as my
>>> system doesnt blow up...
>>>
>>
>> IMHO simply not blowing up tells you nothing.  I can show you a dozen
>> simulations that don't blow up that have terrible small molecule topologies
>> that produce bad results.
>>
>> Parametrization methods and validation procedures are defined in the
>> literature and one could easily fill a book chapter (or more) on such
>> topics, so I will not go into it in an email.  You may have to go back
>> several years (or even decades) in the literature to get the full story.
>>
>>
>>  And what do you mean "thourough parametrization?
>>>
>>
>> Most people hope for a simple, one-shot step they can take to parametrize
>> a small molecule.  There are numerous "black box" methods out there, some
>> good and some bad.  I advise people to be thorough in terms of what the
>> force field requires and what their chemical knowledge tells them.  For
>> instance, for water interactions in CHARMM, HF/6-31G* works well for most
>> compounds, unless sulfur is involved, in which case we need to do a more
>> expensive MP2/6-31G* calculation.  You can get an OK result for everything
>> with HF, but it's not sufficiently accurate in all cases.
>>
>>
>>  I parametrized flavin mononucleotide using amber99sb-ildn, I used
>>> existing
>>> atomtypes in the force field, but I added partial atomic charges based
>>> on a
>>> decent DFT calculation in orca, and I had to add 2 distance restraints on
>>> the delta negatively charged phosphate oxygens to keep them from crashing
>>> into the delta positive hydrogen on the same phosphate. Is that thorough
>>> in
>>> your opinion?
>>>
>>
>> How does it compare with the results of running the molecule through
>> antechamber?  Usually GAFF gives a reasonable topology with minimal
>> adjustment necessary.  That's one of the benefits of Amber; there are very
>> well-defined protocols and a robust general force field for the
>> parametrization.
>>
>> -Justin
>>
>>
>> --
>> ==**
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul@outerbanks.umaryland.**edu | 
>> (410)
>> 706-7441
>>
>> ==**
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
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>
>
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Re: [gmx-users] changing atom types versus adding dihedrals to atom types

[Rafael I. Silverman y de la Vega]

Hmm, I will have to do some more controls then, but I  prob dont have time
to do them till after quals this fall...
You mention Hartree-Fock methods, does this mean that you disfavor DFT for
some reason for this purpose?


On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul  wrote:

>
>
> On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote:
>
>> Can you give some examples of how these verifications are  different for
>> different force fields? It doesnt seem like verifying takes that much
>> time,
>> but a theorist prof in my department told me not to worry as long as my
>> system doesnt blow up...
>>
>
> IMHO simply not blowing up tells you nothing.  I can show you a dozen
> simulations that don't blow up that have terrible small molecule topologies
> that produce bad results.
>
> Parametrization methods and validation procedures are defined in the
> literature and one could easily fill a book chapter (or more) on such
> topics, so I will not go into it in an email.  You may have to go back
> several years (or even decades) in the literature to get the full story.
>
>
>  And what do you mean "thourough parametrization?
>>
>
> Most people hope for a simple, one-shot step they can take to parametrize
> a small molecule.  There are numerous "black box" methods out there, some
> good and some bad.  I advise people to be thorough in terms of what the
> force field requires and what their chemical knowledge tells them.  For
> instance, for water interactions in CHARMM, HF/6-31G* works well for most
> compounds, unless sulfur is involved, in which case we need to do a more
> expensive MP2/6-31G* calculation.  You can get an OK result for everything
> with HF, but it's not sufficiently accurate in all cases.
>
>
>  I parametrized flavin mononucleotide using amber99sb-ildn, I used existing
>> atomtypes in the force field, but I added partial atomic charges based on
>> a
>> decent DFT calculation in orca, and I had to add 2 distance restraints on
>> the delta negatively charged phosphate oxygens to keep them from crashing
>> into the delta positive hydrogen on the same phosphate. Is that thorough
>> in
>> your opinion?
>>
>
> How does it compare with the results of running the molecule through
> antechamber?  Usually GAFF gives a reasonable topology with minimal
> adjustment necessary.  That's one of the benefits of Amber; there are very
> well-defined protocols and a robust general force field for the
> parametrization.
>
> -Justin
>
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
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Re: [gmx-users] changing atom types versus adding dihedrals to atom types

[Rafael I. Silverman y de la Vega]

Can you give some examples of how these verifications are  different for
different force fields? It doesnt seem like verifying takes that much time,
but a theorist prof in my department told me not to worry as long as my
system doesnt blow up...
And what do you mean "thourough parametrization?
I parametrized flavin mononucleotide using amber99sb-ildn, I used existing
atomtypes in the force field, but I added partial atomic charges based on a
decent DFT calculation in orca, and I had to add 2 distance restraints on
the delta negatively charged phosphate oxygens to keep them from crashing
into the delta positive hydrogen on the same phosphate. Is that thorough in
your opinion?
Thanks

On Thu, Sep 12, 2013 at 7:32 PM, Justin Lemkul  wrote:

>
>
> On 9/12/13 7:04 PM, Rafael I. Silverman y de la Vega wrote:
>
>> I see,
>>   when you say thorough parametrization and validation, what do you mean?
>> How does one validate the system, calculate free energy in solution and
>> compare it to tabulated data?
>>
>>
> The target data depend on the force field for which parameters are being
> developed.  Matching QM geometries, water interaction energies and
> distances, free energies of solvation, crystal structures, liquid
> properties, etc. are all useful depending on the underlying force field and
> how it was derived.  For bonded parameters, matching QM energy scans and/or
> vibrational properties are common.
>
> -Justin
>
>
>> On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote:
>>>
>>>  Hi all,
>>>> in another thread it was recommended that instead of changing the atom
>>>> types by analogy to ones with the desired parameter already assigned,
>>>> that
>>>> instead one should assign bonded parameters by analogy.  I was just
>>>> wondering how this is better?
>>>>
>>>>
>>> I didn't suggest that.  I said that any assignment by analogy can have
>>> negative outcomes.  Bonds and angles, in theory, are a bit easier to deal
>>> with because the nonbonded interactions between their atoms are excluded.
>>>   Torsions are very difficult because the torsional bonded terms have to
>>> be
>>> balanced against the charge and LJ parameters of atoms separated by 3
>>> bonds, i.e. 1-4 interactions.
>>>
>>> Let me state very clearly that, for any missing parameters, anything
>>> short
>>> of a thorough parametrization and validation is (in my purist mind)
>>> unsound.
>>>
>>>
>>> As long as the atom type isnt too different, then why would the
>>> torsions
>>>
>>>> not work out right? If the parameters are interrelated, what makes it
>>>> better to add one term to an atom type rather than changing all the
>>>> terms
>>>> (to ones that are supposed to be together)?
>>>>
>>>>
>>>>  The key is being sufficiently similar, but even subtle differences
>>> between
>>> LJ parameters have very large consequences, especially for 1-4
>>> interactions, so I find it hard to believe that one will recapitulate
>>> accurate interactions in this case.  Of course, all assignments by
>>> analogy
>>> bear some penalty for nonequivalent groups.  I balked at your initial
>>> post
>>> in the other thread because there was no need to mess with atom types.
>>>  The
>>> system at hand there contained protein and lipid and could be completely
>>> described by existing atom types and bonded types, the OP there was just
>>> (and perhaps still is) constructing the force field incorrectly.  I felt
>>> it
>>> need to be stated that the approach there would not necessarily be
>>> productive, and to make sure the archive was complete so that no one
>>> would
>>> come across a post in vacuum and assume that he or she can simply swap
>>> around atom types to make error messages go away.  Your initial statement
>>> referred only to bonds and angles, which indeed would be insensitive to
>>> changes in LJ parameters on any of those atoms, but since the thread was
>>> in
>>> the context of dihedrals, I thought I should state my opinion there.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> Sch

Re: [gmx-users] changing atom types versus adding dihedrals to atom types

[Rafael I. Silverman y de la Vega]

I see,
 when you say thorough parametrization and validation, what do you mean?
How does one validate the system, calculate free energy in solution and
compare it to tabulated data?


On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul  wrote:

>
>
> On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote:
>
>> Hi all,
>> in another thread it was recommended that instead of changing the atom
>> types by analogy to ones with the desired parameter already assigned, that
>> instead one should assign bonded parameters by analogy.  I was just
>> wondering how this is better?
>>
>
> I didn't suggest that.  I said that any assignment by analogy can have
> negative outcomes.  Bonds and angles, in theory, are a bit easier to deal
> with because the nonbonded interactions between their atoms are excluded.
>  Torsions are very difficult because the torsional bonded terms have to be
> balanced against the charge and LJ parameters of atoms separated by 3
> bonds, i.e. 1-4 interactions.
>
> Let me state very clearly that, for any missing parameters, anything short
> of a thorough parametrization and validation is (in my purist mind) unsound.
>
>
>As long as the atom type isnt too different, then why would the torsions
>> not work out right? If the parameters are interrelated, what makes it
>> better to add one term to an atom type rather than changing all the terms
>> (to ones that are supposed to be together)?
>>
>>
> The key is being sufficiently similar, but even subtle differences between
> LJ parameters have very large consequences, especially for 1-4
> interactions, so I find it hard to believe that one will recapitulate
> accurate interactions in this case.  Of course, all assignments by analogy
> bear some penalty for nonequivalent groups.  I balked at your initial post
> in the other thread because there was no need to mess with atom types.  The
> system at hand there contained protein and lipid and could be completely
> described by existing atom types and bonded types, the OP there was just
> (and perhaps still is) constructing the force field incorrectly.  I felt it
> need to be stated that the approach there would not necessarily be
> productive, and to make sure the archive was complete so that no one would
> come across a post in vacuum and assume that he or she can simply swap
> around atom types to make error messages go away.  Your initial statement
> referred only to bonds and angles, which indeed would be insensitive to
> changes in LJ parameters on any of those atoms, but since the thread was in
> the context of dihedrals, I thought I should state my opinion there.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] changing atom types versus adding dihedrals to atom types

[Rafael I. Silverman y de la Vega]

Hi all,
in another thread it was recommended that instead of changing the atom
types by analogy to ones with the desired parameter already assigned, that
instead one should assign bonded parameters by analogy.  I was just
wondering how this is better?
 As long as the atom type isnt too different, then why would the torsions
not work out right? If the parameters are interrelated, what makes it
better to add one term to an atom type rather than changing all the terms
(to ones that are supposed to be together)?
-- 
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Re: [gmx-users] NMR restrained MD

[Rafael I. Silverman y de la Vega]

How so? If there is an atom type that has a reasonable similarity to the
one that doesnt have the default bondtypes, what makes using that worse
than coming up with entirely new parameters that are not necessarily based
on physical data or quantum calculations? Isnt copying angles and force
constants the same thing?


On Tue, Sep 10, 2013 at 10:34 AM, Justin Lemkul  wrote:

>
>
> On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote:
>
>> Adding parameters can be a little bit of a pain, you could instead change
>> the atom types in the molecule parameter, to ones that have defined angles
>> and bond types with each other. Of course, you would need to make sure
>> that
>> you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc.
>> Check out ffbonded in the appropriate forcefield folder to see which
>> atomtypes have defined bond types. Check out atomtypes.atp to see all the
>> atom types for the forcefield
>>
>>
> Given that at present the issue involves only protein and lipids, the
> approach of swapping around atom types is very dangerous, probably more so
> than assigning bonded parameters by analogy.  I don't recall the OP ever
> telling us what the force field is, though, so it's hard to know all of
> what we're dealing with here.
>
> -Justin
>
>
>> On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote:
>>>
>>>  Hi Justin,
>>>>
>>>> It is which part in the force field. Exactly which file I have to look
>>>> to
>>>> overcome this errors.
>>>>
>>>>
>>>>  Go to the line number in the .top indicated in the error message and
>>> determine the atom types.  This will tell you the sequence of atom types
>>> involved in the R-B dihedral that is missing.  In theory, you would then
>>> add missing parameters to ffbonded.itp, if they exist.
>>>
>>> -Justin
>>>
>>>
>>>   On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul 
>>> wrote:
>>>
>>>>
>>>>
>>>>
>>>>> On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote:
>>>>>
>>>>>   Hi Justin,
>>>>>
>>>>>>
>>>>>> This is another type of error while running energy minimization:
>>>>>> what to do for these type of errors.
>>>>>>
>>>>>>
>>>>>>   They're exactly the same as the dihedral error from before.  You're
>>>>>>
>>>>> using
>>>>> parameters that don't exist in the force field.
>>>>>
>>>>> -Justin
>>>>>
>>>>>ERROR 218 [file topol.top, line 23487]:
>>>>>
>>>>>   No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 219 [file topol.top, line 23499]:
>>>>>>  No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 220 [file topol.top, line 23500]:
>>>>>>  No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 221 [file topol.top, line 23501]:
>>>>>>  No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 222 [file topol.top, line 23502]:
>>>>>>  No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 223 [file topol.top, line 23503]:
>>>>>>  No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> ERROR 224 [file topol.top, line 23515]:
>>>>>>  No default Ryckaert-Bell. types
>>>>>>
>>>>>>
>>>>>> --Rama
>>>>>>
>>>>>>
>>>>>> On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul 
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>  On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote:
>>>>>>>
>>>>>>>Hi Justin,
>>>>>>>
>>>>>>>
>>>>>>>> I included 1 DMPC molecule parameters in the file should I need to
>>>>>>>> include
>>>>>>>> 128 molecules parameters in the file .rtp.
>>>>>>>>
>>>

Re: [gmx-users] NMR restrained MD

[Rafael I. Silverman y de la Vega]

Adding parameters can be a little bit of a pain, you could instead change
the atom types in the molecule parameter, to ones that have defined angles
and bond types with each other. Of course, you would need to make sure that
you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc.
Check out ffbonded in the appropriate forcefield folder to see which
atomtypes have defined bond types. Check out atomtypes.atp to see all the
atom types for the forcefield


On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul  wrote:

>
>
> On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote:
>
>> Hi Justin,
>>
>> It is which part in the force field. Exactly which file I have to look to
>> overcome this errors.
>>
>>
> Go to the line number in the .top indicated in the error message and
> determine the atom types.  This will tell you the sequence of atom types
> involved in the R-B dihedral that is missing.  In theory, you would then
> add missing parameters to ffbonded.itp, if they exist.
>
> -Justin
>
>
>  On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote:
>>>
>>>  Hi Justin,

 This is another type of error while running energy minimization:
 what to do for these type of errors.


  They're exactly the same as the dihedral error from before.  You're
>>> using
>>> parameters that don't exist in the force field.
>>>
>>> -Justin
>>>
>>>   ERROR 218 [file topol.top, line 23487]:
>>>
 No default Ryckaert-Bell. types


 ERROR 219 [file topol.top, line 23499]:
 No default Ryckaert-Bell. types


 ERROR 220 [file topol.top, line 23500]:
 No default Ryckaert-Bell. types


 ERROR 221 [file topol.top, line 23501]:
 No default Ryckaert-Bell. types


 ERROR 222 [file topol.top, line 23502]:
 No default Ryckaert-Bell. types


 ERROR 223 [file topol.top, line 23503]:
 No default Ryckaert-Bell. types


 ERROR 224 [file topol.top, line 23515]:
 No default Ryckaert-Bell. types


 --Rama


 On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul  wrote:



> On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote:
>
>   Hi Justin,
>
>>
>> I included 1 DMPC molecule parameters in the file should I need to
>> include
>> 128 molecules parameters in the file .rtp.
>>
>>
>>   No.  Residue definitions are used any time they are encountered in
>> the
>>
> coordinate file.  There is no need for such redundancy at the force
> field
> level.
>
>
> -Justin
>
> --
> ==**
>
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  umaryland.edu 
> >>
> | (410)
> 706-7441
>
> ==**
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> http://lists.gromacs.org/**mailman/listinfo/gmx-users>
> >
> http://lists.gromacs.org/mailman/**listinfo/gmx-users>
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >
>
>>
>>  * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<**h**ttp://www.gromacs.org/**Support/**
> Mailing_Lists/Search Mailing_Lists/Search
> >>before
> posting!
>
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
> 
> >
> 
> http://www.gromacs.org/Support/Mailing_Lists>
> >
>
>>
>>
>
>  --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul@outerbanks.umaryland.edu >> umaryland.edu > | (410)
>>> 706-7441
>>>
>>> ==
>>> --
>>> gmx-u

Re: [gmx-users] simulation explode while switching from NVT to NPT

[Rafael I. Silverman y de la Vega]

Did you follow the link in the error message?


On Wed, Sep 4, 2013 at 7:17 PM, Golshan Hejazi wrote:

> Hi everyone,
>
> I am simulating a system of paracetamol crystal in ethanol solvent. I used
> pdb2gmx to generate the topology and gro file and I minimized the system
> using steepest decent. As long as I perform NVT simulations at any
> temperature, the simulations goes on! But as soon as I switch from NVT to
> NPT, the simulation crashes with the following error:
>
> I tried to perform NVT at very low temperature, say 50K and then switch to
> NPT ... but no WAY!
> Can you help me with that?
>
> Thanks
>
> Warning: 1-4 interaction between 1361 and 1368 at distance
> 10600663849073184.000 which is larger than the 1-4 table size 1.800 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> ---
> Program mdrun, VERSION 4.5.4
> Source code file: pme.c, line: 538
>
> Fatal error:
> 9 particles communicated to PME node 0 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
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Re: [gmx-users] Distance restraints exploding system

[Rafael I. Silverman y de la Vega]

Have you tried with even less restraints? I found systems are not always
stable with more than the bare minimum of restraints


On Sun, Sep 1, 2013 at 7:54 PM, Trayder Thomas wrote:

> It still explodes on a 0.1fs timestep, turning off P-R doesn't seem to have
> an impact. I've tried being gentle, slowly turning up the force constant
> and running for 1 ns for each value but as soon as the force constant
> approaches 100 it crashes.
> The starting structure was generated with the same restraints, so it is
> very close. I have tried using slightly different starting structures as
> well.
>
> I've tried running it with only 3 restraints (1 methyl group to 1 hydrogen
> with the restraints extended by 0.2nm so that all hydrogens are within the
> restraint distance) and I'm getting a segmentation fault (no LINCS
> warnings) at 100 steps. It runs fine with any combination of 2 hydrogens
> restrained, but as soon as I restrain the 3rd one I get a segmentation
> fault (this occurs with either setting for disre-weighting). So it seems to
> fair better with more restraints?
>
> The more I try to solve this problem the less it makes sense!
>
> -Trayder
>
>
> On Fri, Aug 30, 2013 at 6:02 PM, Mark Abraham  >wrote:
>
> > On Fri, Aug 30, 2013 at 8:56 AM, Trayder 
> > wrote:
> > > Hello,
> > > I am attempting to simulate a protein-ligand complex using distance
> > > restraints to match it to NMR data.
> > > The system runs stably without restraints. With restraints it tends to
> > spit
> > > out LINCS angle warnings and blow up under most conditions.
> > >
> > > I'm attempting to use:
> > > ;   Restraints
> > > disre   =  simple
> > > disre-weighting =  conservative
> > > disre-fc=  1000
> > >
> > > It blows up within 100 steps unless:
> > > I run on a single core (+gpu) or
> > > disre-fc = <100 or
> > > disre-weighting = equal
> > >
> > > If disre-weighting = conservative is causing extreme forces, then I
> > figure
> > > it should do the same on 1 core.
> >
> > Not really. MD is chaotic. Small changes in initial conditions lead to
> > different results.
> >
> > > If domain decomposition is the problem, then I would think
> > disre-weighting =
> > > equal shouldn't work either.
> > > I'm stumped... anyone got any ideas?
> >
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up has the
> > usual suggestions - don't use P-R yet, try a smaller time step, make
> > sure your system is close to the restrained regime (or be extra gentle
> > until it is).
> >
> > Mark
> >
> > > Thanks in advance,
> > > -Trayder
> > >
> > > Distance restraints excerpt:
> > > ; aiaj  typeindex   type’   low up1 up2 fac
> > > ; 2 symmetric hydrogens
> > >  1306  1389 1   10  1   0.0 0.548   1.0 1.0
> > >  1306  1396 1   10  1   0.0 0.548   1.0 1.0
> > > ; Diastereotopic methyl groups
> > >  1306  1374 1   11  1   0.0 0.654   1.0 1.0
> > >  1306  1375 1   11  1   0.0 0.654   1.0 1.0
> > >  1306  1376 1   11  1   0.0 0.654   1.0 1.0
> > >  1306  1385 1   11  1   0.0 0.654   1.0 1.0
> > >  1306  1386 1   11  1   0.0 0.654   1.0 1.0
> > >  1306  1387 1   11  1   0.0 0.654   1.0 1.0
> > >
> > > Full mdp:
> > > ;   Run Control
> > > integrator  =  md  ; simulation algorithm
> > > tinit= 0
> > > dt   = 0.002
> > > nsteps  =  50
> > > ;
> > > ;   Output Control
> > > nstxout =  20; write coordinates to
> > .trr
> > > nstvout =  20; write velocities to
> > .trr
> > > nstlog  =  1000 ; write energies to
> .log
> > > nstenergy   =  4000 ; write energies to
> .edr
> > > nstxtcout   =  1000  ; write coordinates to
> > .xtc
> > > ;
> > > ;   Neighbour Searching
> > > nstlist =  10   ; update neighbour list
> > > ns_type =  grid ; neighbour list method
> > > pbc =  xyz  ; periodic boundary
> > > conditions
> > > rlist   =  0.9  ; cut-off for
> short-range
> > > neighbour (nm)
> > > cutoff-scheme   =  verlet
> > > ;
> > > ;   Electrostatics and VdW
> > > coulombtype =  PME  ; type of coulomb
> > > interaction
> > > rcoulomb=  0.9  ; cut-off distance for
> > > coulomb
> > > epsilon_r   =  1; dielectric constant
> > > rvdw=  0.9  ; cut-off for vdw
> > > fourierspacing  =  0.12 ; maximum grid spacing
> > for
> > > FFT
> > > pme_order   =  4; interpolation order
> f

Re: [gmx-users] TPIC and GMX_TPI_DUMP

[Rafael I. Silverman y de la Vega]

Thanks!
 I will try these latest suggestions!


On Fri, Aug 30, 2013 at 7:27 PM, Rafael I. Silverman y de la Vega <
rsilv...@ucsc.edu> wrote:

> Yes, I hand edited the .tpr file to get the thing to work, otherwise I got
> errors with particle numbers being different.
>
>
> On Fri, Aug 30, 2013 at 6:54 PM, João M. Damas wrote:
>
>> Sorry, where I said "put it as the last coordinate on the .tpr file you're
>> building" it should be "put it as the last coordinate of each frame of the
>> .trr file". You'll need to do some trajectory "hand-editing".
>>
>> João
>>
>>
>> On Sat, Aug 31, 2013 at 2:41 AM, João M. Damas 
>> wrote:
>>
>> > Oh, you were talking about the Energy Distribution output (-tpid),
>> sorry.
>> > So, I haven't used much this output, but from what I see, that energies
>> > histogram is going indefinitely. It seems like a bug in the calculation
>> of
>> > the energy bins, and my intuition is telling me that it has something
>> to do
>> > with the volume correction.. Maybe?
>> >
>> > My suspicion starts with you saying that you are centering the
>> prosthetic
>> > group at 0,0,0. That's not the regular procedure for tpi insertions. The
>> > regular procedure is to center the molecule to insert at 0,0,0. About
>> the
>> > system, you should calculate the average geometric center of the
>> prosthetic
>> > group and use it as the center for insertion! (put it as the last
>> > coordinate on the .tpr file you're building, see the manual). In short:
>> be
>> > careful with your trjconv command and maintain the integrity of the
>> > trajectory (PBC, wholeness, for example).
>> >
>> > Best,
>> > João
>> >
>> >
>> > On Sat, Aug 31, 2013 at 1:30 AM, Rafael I. Silverman y de la Vega <
>> > rsilv...@ucsc.edu> wrote:
>> >
>> >> I am centering the insertion on the prosthetic group, which I put as 0
>> 0
>> >> 0.
>> >> I have a 222 amino acid protein, in maybe .2 M NaCl, I parametrized
>> flavin
>> >> mononucleotide, which sits inside the protein.
>> >>
>> >> I got the .pdb files written, I was setting the GMX_TPI_DUMP in a
>> >> different
>> >> terminal window. Dumb mistake.
>> >>
>> >> Here is the first 100 lines from the xvg. The lines go on for a LONG
>> way
>> >> # This file was created Fri Aug 30 16:54:06 2013
>> >> # by the following command:
>> >> # mdrun -s tpic.tpr -rerun tpic_in.trr -deffnm tpic -nt 1
>> >> #
>> >> # mdrun is part of G R O M A C S:
>> >> #
>> >> # GROtesk MACabre and Sinister
>> >> #
>> >> @title "TPI energy distribution"
>> >> @xaxis  label "\xb\f{}U - log(V/)"
>> >> @yaxis  label "count"
>> >> @TYPE xy
>> >> @ subtitle "number \xb\f{}U > 50: 1.996e+03"
>> >> @ view 0.15, 0.15, 0.75, 0.85
>> >> @ legend on
>> >> @ legend box on
>> >> @ legend loctype view
>> >> @ legend 0.78, 0.8
>> >> @ legend length 2
>> >> @ s0 legend "direct"
>> >> @ s1 legend "reweighted"
>> >> -1445442.50  0 -nan
>> >> -1445442.40  0 -nan
>> >> -1445442.30  0 -nan
>> >> -1445442.20  0 -nan
>> >> -1445442.10  0 -nan
>> >> -1445442.00  0 -nan
>> >> -1445441.90  0 -nan
>> >> -1445441.80  0 -nan
>> >> -1445441.70  0 -nan
>> >> -1445441.60  1 -nan
>> >> -1445441.50  0 -nan
>> >> -1445441.40  0 -nan
>> >> -1445441.30  0 -nan
>> >> -1445441.20  0 -nan
>> >> -1445441.10  0 -nan
>> >> -1445441.00  0 -nan
>> >> -1445440.90  0 -nan
>> >> -1445440.80  0 -nan
>> >> -1445440.70  0 -nan
>> >> -1445440.60  0 -nan
>> >> -1445440.50  0 -nan
>> >> -1445440.40  0 -nan
>> >> -1445440.30  0 -nan
>> >> -1445440.20  0 -nan
>>

Re: [gmx-users] TPIC and GMX_TPI_DUMP

[Rafael I. Silverman y de la Vega]

Yes, I hand edited the .tpr file to get the thing to work, otherwise I got
errors with particle numbers being different.


On Fri, Aug 30, 2013 at 6:54 PM, João M. Damas  wrote:

> Sorry, where I said "put it as the last coordinate on the .tpr file you're
> building" it should be "put it as the last coordinate of each frame of the
> .trr file". You'll need to do some trajectory "hand-editing".
>
> João
>
>
> On Sat, Aug 31, 2013 at 2:41 AM, João M. Damas 
> wrote:
>
> > Oh, you were talking about the Energy Distribution output (-tpid), sorry.
> > So, I haven't used much this output, but from what I see, that energies
> > histogram is going indefinitely. It seems like a bug in the calculation
> of
> > the energy bins, and my intuition is telling me that it has something to
> do
> > with the volume correction.. Maybe?
> >
> > My suspicion starts with you saying that you are centering the prosthetic
> > group at 0,0,0. That's not the regular procedure for tpi insertions. The
> > regular procedure is to center the molecule to insert at 0,0,0. About the
> > system, you should calculate the average geometric center of the
> prosthetic
> > group and use it as the center for insertion! (put it as the last
> > coordinate on the .tpr file you're building, see the manual). In short:
> be
> > careful with your trjconv command and maintain the integrity of the
> > trajectory (PBC, wholeness, for example).
> >
> > Best,
> > João
> >
> >
> > On Sat, Aug 31, 2013 at 1:30 AM, Rafael I. Silverman y de la Vega <
> > rsilv...@ucsc.edu> wrote:
> >
> >> I am centering the insertion on the prosthetic group, which I put as 0 0
> >> 0.
> >> I have a 222 amino acid protein, in maybe .2 M NaCl, I parametrized
> flavin
> >> mononucleotide, which sits inside the protein.
> >>
> >> I got the .pdb files written, I was setting the GMX_TPI_DUMP in a
> >> different
> >> terminal window. Dumb mistake.
> >>
> >> Here is the first 100 lines from the xvg. The lines go on for a LONG way
> >> # This file was created Fri Aug 30 16:54:06 2013
> >> # by the following command:
> >> # mdrun -s tpic.tpr -rerun tpic_in.trr -deffnm tpic -nt 1
> >> #
> >> # mdrun is part of G R O M A C S:
> >> #
> >> # GROtesk MACabre and Sinister
> >> #
> >> @title "TPI energy distribution"
> >> @xaxis  label "\xb\f{}U - log(V/)"
> >> @yaxis  label "count"
> >> @TYPE xy
> >> @ subtitle "number \xb\f{}U > 50: 1.996e+03"
> >> @ view 0.15, 0.15, 0.75, 0.85
> >> @ legend on
> >> @ legend box on
> >> @ legend loctype view
> >> @ legend 0.78, 0.8
> >> @ legend length 2
> >> @ s0 legend "direct"
> >> @ s1 legend "reweighted"
> >> -1445442.50  0 -nan
> >> -1445442.40  0 -nan
> >> -1445442.30  0 -nan
> >> -1445442.20  0 -nan
> >> -1445442.10  0 -nan
> >> -1445442.00  0 -nan
> >> -1445441.90  0 -nan
> >> -1445441.80  0 -nan
> >> -1445441.70  0 -nan
> >> -1445441.60  1 -nan
> >> -1445441.50  0 -nan
> >> -1445441.40  0 -nan
> >> -1445441.30  0 -nan
> >> -1445441.20  0 -nan
> >> -1445441.10  0 -nan
> >> -1445441.00  0 -nan
> >> -1445440.90  0 -nan
> >> -1445440.80  0 -nan
> >> -1445440.70  0 -nan
> >> -1445440.60  0 -nan
> >> -1445440.50  0 -nan
> >> -1445440.40  0 -nan
> >> -1445440.30  0 -nan
> >> -1445440.20  0 -nan
> >> -1445440.10  0 -nan
> >> -1445440.00  0 -nan
> >> -1445439.90  0 -nan
> >> -1445439.80  0 -nan
> >> -1445439.70  0 -nan
> >> -1445439.60  0 -nan
> >> -1445439.50  0 -nan
> >> -1445439.40  0 -nan
> >> -1445439.30  0 -nan
> >> -1445439.20  0 -nan
> >> -1445439.10  0 -nan
> >> -1445439.00  0 -n

Re: [gmx-users] TPIC and GMX_TPI_DUMP

[Rafael I. Silverman y de la Vega]

I am centering the insertion on the prosthetic group, which I put as 0 0 0.
I have a 222 amino acid protein, in maybe .2 M NaCl, I parametrized flavin
mononucleotide, which sits inside the protein.

I got the .pdb files written, I was setting the GMX_TPI_DUMP in a different
terminal window. Dumb mistake.

Here is the first 100 lines from the xvg. The lines go on for a LONG way
# This file was created Fri Aug 30 16:54:06 2013
# by the following command:
# mdrun -s tpic.tpr -rerun tpic_in.trr -deffnm tpic -nt 1
#
# mdrun is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "TPI energy distribution"
@xaxis  label "\xb\f{}U - log(V/)"
@yaxis  label "count"
@TYPE xy
@ subtitle "number \xb\f{}U > 50: 1.996e+03"
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "direct"
@ s1 legend "reweighted"
-1445442.50  0 -nan
-1445442.40  0 -nan
-1445442.30  0 -nan
-1445442.20  0 -nan
-1445442.10  0 -nan
-1445442.00  0 -nan
-1445441.90  0 -nan
-1445441.80  0 -nan
-1445441.70  0 -nan
-1445441.60  1 -nan
-1445441.50  0 -nan
-1445441.40  0 -nan
-1445441.30  0 -nan
-1445441.20  0 -nan
-1445441.10  0 -nan
-1445441.00  0 -nan
-1445440.90  0 -nan
-1445440.80  0 -nan
-1445440.70  0 -nan
-1445440.60  0 -nan
-1445440.50  0 -nan
-1445440.40  0 -nan
-1445440.30  0 -nan
-1445440.20  0 -nan
-1445440.10  0 -nan
-1445440.00  0 -nan
-1445439.90  0 -nan
-1445439.80  0 -nan
-1445439.70  0 -nan
-1445439.60  0 -nan
-1445439.50  0 -nan
-1445439.40  0 -nan
-1445439.30  0 -nan
-1445439.20  0 -nan
-1445439.10  0 -nan
-1445439.00  0 -nan
-1445438.90  0 -nan
-1445438.80  0 -nan
-1445438.70  0 -nan
-1445438.60  0 -nan
-1445438.50  0 -nan
-1445438.40  0 -nan
-1445438.30  0 -nan
-1445438.20  0 -nan
-1445438.10  0 -nan
-1445438.00  0 -nan
-1445437.90  0 -nan
-1445437.80  0 -nan
-1445437.70  0 -nan
-1445437.60  0 -nan
-1445437.50  0 -nan
-1445437.40  0 -nan
-1445437.30  0 -nan
-1445437.20  0 -nan
-1445437.10  0 -nan
-1445437.00  0 -nan
-1445436.90  0 -nan
-1445436.80  0 -nan
-1445436.70  0 -nan
-1445436.60  0 -nan
-1445436.50  0 -nan
-1445436.40  0 -nan
-1445436.30  0 -nan
-1445436.20  0 -nan
-1445436.10  0 -nan
-1445436.00  0 -nan
-1445435.90  0 -nan
-1445435.80  0 -nan
-1445435.70  0 -nan
-1445435.60  0 -nan
-1445435.50  0 -nan
-1445435.40  0 -nan
-1445435.30  0 -nan
-1445435.20  0 -nan
-1445435.10  0 -nan
-1445435.00  0 -nan
-1445434.90  0 -nan
-1445434.80  0 -nan
-1445434.70  0 -nan


On Fri, Aug 30, 2013 at 5:19 PM, João M. Damas  wrote:

> PBC is on works, so the centering is not important. My question had to do
> with the center of insertion: random for tpi, specific for tpic.
>
> That's really my second guess, the infinite energies. The tpi code has a
> way to deal with them internally. Run the insertion [mdrun] with "-debug 1"
> flag and see how many non-finite energies do you hit. Maybe all (number of
> frames times the number of insertions?
>
> Can you post 100 lines or so of your .xvg file? I'm curious about it. Maybe
> 4.6.3 has some new output I'm unaware of.
>
> Also, can you tell something more about your system?
>
> Best,
> João
>
>
> On Sat, Aug 31, 2013 at 12:55 AM, Rafael I. Silverman y de la Vega <
> rsilv...@ucsc.edu> wrote:
>
> > Thanks for the reply João,
> > I am using gromacs 4.6.3, I did centre all 4 frames at the prosthetic
> > group.
> > I tried GMX_TPI_DUMP = 5.0e+3, 5.0e+20, and even 5.0e-03, still, not a
> > single .pdb file written.
> > I am doing this on a 4 frame trajectory, consisting of ~7

Re: [gmx-users] TPIC and GMX_TPI_DUMP

[Rafael I. Silverman y de la Vega]

Thanks for the reply João,
I am using gromacs 4.6.3, I did centre all 4 frames at the prosthetic
group.
I tried GMX_TPI_DUMP = 5.0e+3, 5.0e+20, and even 5.0e-03, still, not a
single .pdb file written.
I am doing this on a 4 frame trajectory, consisting of ~7000 atoms per
frame. I think it may have to do with the frames that have infinite
chemical potential with the insertion? It doesnt seem to have anything to
do with TPI_DUMP, when I lower rtpi to 0.05 the .xvg file becomes less
ridiculously large, only 0.5 gigs...
I suppose I need to try an older version of gromacs, and see if my setup
works there
--
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[gmx-users] TPIC and GMX_TPI_DUMP

[Rafael I. Silverman y de la Vega]

Hi all,
I am trying to insert a water into a prosthetic group binding cavity. I
cant seem to get an output .pdb file of the insertions, I set GMX_TPI_DUMP
in my shell with $ export GMX_TPI_DUMP=xxx but no numbers seemed to work. I
cant really get good information out of the .xvg output either, it always
ends up being like 2+ gigs, and is basically unreadable, plus, writing this
file takes a long time, and gums up the processors.

So 2 questions, can I suppress the writing of the .xvg file, and how do I
get GMX_TPI_DUMP set correctly?
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Re: [gmx-users] Help with Error Message

[Rafael I. Silverman y de la Vega]

a text editor


On Tue, Aug 27, 2013 at 1:54 PM, The One And Only wrote:

> What kind of editor should I open it in? I have Pymol, but I don't know if
> it's the right one.
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Re: [gmx-users] Help with Error Message

[Rafael I. Silverman y de la Vega]

It sounds like you dont have the .pdb file in your working directory.
Perhaps you need to learn a bit about unix filesystems


On Sat, Aug 24, 2013 at 6:18 PM, The One And Only wrote:

> So I started following some tutorials online since I didn't get a response
> last time. the tutorial I'm using is:
> http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/
> I followed that tutorial to the second page and got stuck at the step where
> it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p protein.top
> -ignh
> I picked GROMOS96 45a3 force field(11) for the force field and spc(1) for
> the water model but got the following error message:
> Opening force field file
> /usr/local/gromacs/share/gromacs/top/gromos45a3.ff/aminoacids.r2b
> Reading protein.pdb...
>
> ---
> Program pdb2gmx, VERSION 4.6.3
> Source code file:
> /Users/christinalin/wget-1.14/gromacs-4.6.3/src/gmxlib/futil.c, line: 593
>
> File input/output error:
> protein.pdb
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Help please?
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