[gmx-users] gmx chi: chi.log output all rotamers always 0

[Ebert Maximilian]

hi list,

using gmx chi -s file.tpr -f file.xtc -maxchi 1 -all -g -o i try to get the 
different rotamers and transition between them per ns. however, the chi.log 
output file has for every residue only this:

Residue LYS12
Angle [   AI,   AJ,   AK,   AL]  rotamers  0  g(-)  t  g(+)

  Chi1[ 120, 122, 124, 127]0.000.000.000.00


any idea why? the xtc file is aligned and pbc was solved beforehand.

Thank you very much,

Max
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 141, Issue 93

[Justin Lemkul]

On 1/22/16 3:08 PM, lloyd riggs wrote:

Dear Ganesh,
You can also use the ATB site, and convert the all atom .itp to CHARM36 format,
or build it (charge, bond, angles, etc...) from the already present CHARMM36
atom parameters.  Check your charges if you get them from the ATB.


Any parameters from ATB will be completely incompatible with CHARMM.  Also note 
that GROMOS (united-atom) and CHARMM (all-atom) are fundamentally different so 
such conversion is actually impossible, anyway.


-Justin


Stephan Watkins
On 1/22/16 8:51 AM, Ganesh Shahane wrote:
 > Dear Gromacs users,
 >
 > I wish to simulate a mixed lipid bilayer of which one of the lipids is
 > sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using Charmm36
 > ff. Towards this, I constructed the bilayer using Charmm-GUI but then was
 > surprised to find that its topology is not present in residue topology
 > database of Charmm36 ff.
 >
 > Does anyone has any idea about where can I get topology for PSM? Or would
 > it be wise to submit it to paramchem to get its topology?
 >

Use the force field CHARMM-GUI provides you. It supports everything in your
system. Our charmm36.ff port may not include everything; I extend it only when
people ask for specific parameters (as CHARMM is a huge force field, sometimes
things get missed and I rely on this kind of feedback). I'll add sphingomyelin
in the next release.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


==


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End of gromacs.org_gmx-users Digest, Vol 141, Issue 93
**
**




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] trivial question about water molecules

[Justin Lemkul]

Please keep the discussion on the gmx-users mailing list.

On 1/22/16 3:42 AM, Marta Wisniewska wrote:

Hello Justin,

thank you for your response. I know about that way. I'd like to calculate it on
piece of paper. I'va already tried do this. But I have small problem and the
solutions is not in agreement with data from topolgy file. How can I calculate 
this?



I don't understand what the question is.  How many ions were added?  What data 
do you think are in disagreement?  genion really does a very simple operation, 
so it should be quite obvious what happened.  The calculation is nothing more 
than simple arithmetic.


-Justin


Thank you in advance,
Marta

Date: Thu, 21 Jan 2016 12:30:36 -0500
From: Justin Lemkul >
To: gmx-us...@gromacs.org 
Subject: Re: [gmx-users] trivial question about water molecules
Message-ID: <56a115bc.9020...@vt.edu >
Content-Type: text/plain; charset=windows-1252; format=flowed



On 1/21/16 11:47 AM, Marta Wisniewska wrote:
 > Hello Gromacs Users;
 >
 > I'd like to calculate the # of replaced water molecules by sodium chloride
 > in my system . I added a 0.15M concentration of NaCl. How can I calculate
 > the number of water molecules, which are replaced by ions?
 >

genion replaces a water molecule with an ion, so the number of waters replaced
equals the number of ions added.

-Justin


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] does gromac "mdrun" produce predicted 3d structure?

[Arron Lacey]

Hi everyone - I have used I-TASSER to generate pdb files for missense 
SNPs. I understand there are some reservations about the accuracy of SNP 
structural changes by using homology based methods alone. Can GROMACS 
off anything better? I have used


gmx mdrun 

to calculate the energy minimization of the pdb files that I-TASSER 
outputs, but I want to know if mdrun can produce the predicted 
co-ordinates of the structure due to the SNP (if there is any change 
that is)?


Also - does there a better way to embed a SNP in a wild-type pdb file 
for input to pdb2gmx?


Thanks very much.
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Re: [gmx-users] Topology for Sphingomyelin

[Ganesh Shahane]

Hi Justin,

I have stumbled upon another problem. The sphingomyelin topology (PSM.itp)
that Charmm-GUI provides has an atomtype called NHL that is not defined by
the Charmm36 ff. I am using the latest charmm36-jun2015.ff. Could you
please look in to this?

On Fri, Jan 22, 2016 at 4:29 PM, Ganesh Shahane 
wrote:

> Thank you for your reply Justin!. It was helpful.
>
> On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 1/22/16 8:51 AM, Ganesh Shahane wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I wish to simulate a mixed lipid bilayer of which one of the lipids is
>>> sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using
>>> Charmm36
>>> ff. Towards this, I constructed the bilayer using Charmm-GUI but then was
>>> surprised to find that its topology is not present in residue topology
>>> database of Charmm36 ff.
>>>
>>> Does anyone has any idea about where can I get topology for PSM? Or would
>>> it be wise to submit it to paramchem to get its topology?
>>>
>>>
>> Use the force field CHARMM-GUI provides you.  It supports everything in
>> your system.  Our charmm36.ff port may not include everything; I extend it
>> only when people ask for specific parameters (as CHARMM is a huge force
>> field, sometimes things get missed and I rely on this kind of feedback).
>> I'll add sphingomyelin in the next release.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> 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.
>>
>
>
>
> --
> Best Regards,
> Ganesh Shahane
>



-- 
Best Regards,
Ganesh Shahane
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[gmx-users] Topology for Sphingomyelin

[Ganesh Shahane]

Dear Gromacs users,

I wish to simulate a mixed lipid bilayer of which one of the lipids is
sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using Charmm36
ff. Towards this, I constructed the bilayer using Charmm-GUI but then was
surprised to find that its topology is not present in residue topology
database of Charmm36 ff.

Does anyone has any idea about where can I get topology for PSM? Or would
it be wise to submit it to paramchem to get its topology?

Thank you in advance.

-- 
Best Regards,
Ganesh Shahane
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Re: [gmx-users] does gromac "mdrun" produce predicted 3d structure?

[Justin Lemkul]

On 1/22/16 8:05 AM, Arron Lacey wrote:

Hi everyone - I have used I-TASSER to generate pdb files for missense SNPs. I
understand there are some reservations about the accuracy of SNP structural
changes by using homology based methods alone. Can GROMACS off anything better?
I have used

gmx mdrun 

to calculate the energy minimization of the pdb files that I-TASSER outputs, but
I want to know if mdrun can produce the predicted co-ordinates of the structure
due to the SNP (if there is any change that is)?



There is no really simple answer to this, but here are a few things to consider. 
 GROMACS does not predict structures.  It calculates the physical forces on the 
given configuration according to whatever instructions you provide.  Energy 
minimization is certainly insufficient to establish whether or not your mutation 
is structurally reasonable.  You need actual (extensive) MD simulations to 
determine that.  More importantly, the quality of the simulation is only as good 
as the force field you apply for the simulation.  All force fields involve 
assumptions and have some inaccuracy.  So your ability to "predict" using 
GROMACS (I suggest you don't use that term in this context) is only as good as 
(1) the rigor of the method you apply via the MD and (2) the quality of the 
force field in discriminating subtle behaviors.


-Justin


Also - does there a better way to embed a SNP in a wild-type pdb file for input
to pdb2gmx?

Thanks very much.


--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] does gromac "mdrun" produce predicted 3d structure?

[Arron Lacey]

Thanks Justin - you mention

"You need actual (extensive) MD simulations to determine that"

I suppose what I am after is - what software is capable of providing 
such MD simulations?


Thanks!



On 22/01/16 13:13, Justin Lemkul wrote:



On 1/22/16 8:05 AM, Arron Lacey wrote:
Hi everyone - I have used I-TASSER to generate pdb files for missense 
SNPs. I
understand there are some reservations about the accuracy of SNP 
structural
changes by using homology based methods alone. Can GROMACS off 
anything better?

I have used

gmx mdrun 

to calculate the energy minimization of the pdb files that I-TASSER 
outputs, but
I want to know if mdrun can produce the predicted co-ordinates of the 
structure

due to the SNP (if there is any change that is)?



There is no really simple answer to this, but here are a few things to 
consider.  GROMACS does not predict structures.  It calculates the 
physical forces on the given configuration according to whatever 
instructions you provide.  Energy minimization is certainly 
insufficient to establish whether or not your mutation is structurally 
reasonable.  You need actual (extensive) MD simulations to determine 
that.  More importantly, the quality of the simulation is only as good 
as the force field you apply for the simulation.  All force fields 
involve assumptions and have some inaccuracy.  So your ability to 
"predict" using GROMACS (I suggest you don't use that term in this 
context) is only as good as (1) the rigor of the method you apply via 
the MD and (2) the quality of the force field in discriminating subtle 
behaviors.


-Justin

Also - does there a better way to embed a SNP in a wild-type pdb file 
for input

to pdb2gmx?

Thanks very much.




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Re: [gmx-users] Topology for Sphingomyelin

[Justin Lemkul]

On 1/22/16 8:51 AM, Ganesh Shahane wrote:

Dear Gromacs users,

I wish to simulate a mixed lipid bilayer of which one of the lipids is
sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using Charmm36
ff. Towards this, I constructed the bilayer using Charmm-GUI but then was
surprised to find that its topology is not present in residue topology
database of Charmm36 ff.

Does anyone has any idea about where can I get topology for PSM? Or would
it be wise to submit it to paramchem to get its topology?



Use the force field CHARMM-GUI provides you.  It supports everything in your 
system.  Our charmm36.ff port may not include everything; I extend it only when 
people ask for specific parameters (as CHARMM is a huge force field, sometimes 
things get missed and I rely on this kind of feedback).  I'll add sphingomyelin 
in the next release.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations

[Justin Lemkul]

On 1/22/16 10:04 AM, anu chandra wrote:

Dear Gromcas users,

I have been following the Gromcas tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/08_MD.html
) for setting up and running MD simulations of membrane proteins. I am
aiming for a microsecond long simulation. In this regard, I have few
queries about some of the parameters in mdp file used for production run in
membrane protein tutorial.

1. Is it required to use NPT (pressure coupling) rather than NVT for the
production run if the system is already extensively equilbrated in NPT
ensemble before taking to the production stage?



To some extent, this depends on the force field.  NPT is preferred and most 
modern lipid force fields work best with this ensemble.  With NVT, you wind up 
with a constant lipid area, which can impose surface tension.  This may be bad 
for some force fields.



2. The literature suggests to set the random seed generator 'on' for a
better sampling during simulation. I have noticed that the 'gen_vel = no'
in the mdp file used for production run in the tutorial. I just wonder,
will it be safe to set the 'gen_vel=yes' during the production run using
Gromcas.



If you regenerate velocities, what was the point of prior equilibration?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] does gromac "mdrun" produce predicted 3d structure?

[Justin Lemkul]

On 1/22/16 9:35 AM, Arron Lacey wrote:

Thanks Justin - you mention

"You need actual (extensive) MD simulations to determine that"

I suppose what I am after is - what software is capable of providing such MD
simulations?



You've already come to the right place...

-Justin


Thanks!



On 22/01/16 13:13, Justin Lemkul wrote:



On 1/22/16 8:05 AM, Arron Lacey wrote:

Hi everyone - I have used I-TASSER to generate pdb files for missense SNPs. I
understand there are some reservations about the accuracy of SNP structural
changes by using homology based methods alone. Can GROMACS off anything better?
I have used

gmx mdrun 

to calculate the energy minimization of the pdb files that I-TASSER outputs, but
I want to know if mdrun can produce the predicted co-ordinates of the structure
due to the SNP (if there is any change that is)?



There is no really simple answer to this, but here are a few things to
consider.  GROMACS does not predict structures.  It calculates the physical
forces on the given configuration according to whatever instructions you
provide.  Energy minimization is certainly insufficient to establish whether
or not your mutation is structurally reasonable.  You need actual (extensive)
MD simulations to determine that.  More importantly, the quality of the
simulation is only as good as the force field you apply for the simulation.
All force fields involve assumptions and have some inaccuracy.  So your
ability to "predict" using GROMACS (I suggest you don't use that term in this
context) is only as good as (1) the rigor of the method you apply via the MD
and (2) the quality of the force field in discriminating subtle behaviors.

-Justin


Also - does there a better way to embed a SNP in a wild-type pdb file for input
to pdb2gmx?

Thanks very much.






--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] A question about pressure coupling and random seed generator in microsecond long simulations

[anu chandra]

Dear Gromcas users,

I have been following the Gromcas tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/08_MD.html
) for setting up and running MD simulations of membrane proteins. I am
aiming for a microsecond long simulation. In this regard, I have few
queries about some of the parameters in mdp file used for production run in
membrane protein tutorial.

1. Is it required to use NPT (pressure coupling) rather than NVT for the
production run if the system is already extensively equilbrated in NPT
ensemble before taking to the production stage?

2. The literature suggests to set the random seed generator 'on' for a
better sampling during simulation. I have noticed that the 'gen_vel = no'
in the mdp file used for production run in the tutorial. I just wonder,
will it be safe to set the 'gen_vel=yes' during the production run using
Gromcas.


Many thanks in advance

Anu
-- 
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Re: [gmx-users] Topology for Sphingomyelin

[Ganesh Shahane]

Thank you for your reply Justin!. It was helpful.

On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul  wrote:

>
>
> On 1/22/16 8:51 AM, Ganesh Shahane wrote:
>
>> Dear Gromacs users,
>>
>> I wish to simulate a mixed lipid bilayer of which one of the lipids is
>> sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using
>> Charmm36
>> ff. Towards this, I constructed the bilayer using Charmm-GUI but then was
>> surprised to find that its topology is not present in residue topology
>> database of Charmm36 ff.
>>
>> Does anyone has any idea about where can I get topology for PSM? Or would
>> it be wise to submit it to paramchem to get its topology?
>>
>>
> Use the force field CHARMM-GUI provides you.  It supports everything in
> your system.  Our charmm36.ff port may not include everything; I extend it
> only when people ask for specific parameters (as CHARMM is a huge force
> field, sometimes things get missed and I rely on this kind of feedback).
> I'll add sphingomyelin in the next release.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> 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.
>



-- 
Best Regards,
Ganesh Shahane
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Re: [gmx-users] Topology for Sphingomyelin

[Justin Lemkul]

On 1/22/16 7:43 PM, Ganesh Shahane wrote:

Hi Justin,

I have stumbled upon another problem. The sphingomyelin topology (PSM.itp)
that Charmm-GUI provides has an atomtype called NHL that is not defined by
the Charmm36 ff. I am using the latest charmm36-jun2015.ff. Could you
please look in to this?



As I said, the charmm36.ff distribution we provide is not going to work because 
parameters related to sphingolipids will not be there.  But CHARMM-GUI gives you 
an all-inclusive force field file that has everything you need.


-Justin


On Fri, Jan 22, 2016 at 4:29 PM, Ganesh Shahane 
wrote:


Thank you for your reply Justin!. It was helpful.

On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul  wrote:




On 1/22/16 8:51 AM, Ganesh Shahane wrote:


Dear Gromacs users,

I wish to simulate a mixed lipid bilayer of which one of the lipids is
sphingomyelin (PSM, 18:1-sphingosine and 16:0-palmitic acid) using
Charmm36
ff. Towards this, I constructed the bilayer using Charmm-GUI but then was
surprised to find that its topology is not present in residue topology
database of Charmm36 ff.

Does anyone has any idea about where can I get topology for PSM? Or would
it be wise to submit it to paramchem to get its topology?



Use the force field CHARMM-GUI provides you.  It supports everything in
your system.  Our charmm36.ff port may not include everything; I extend it
only when people ask for specific parameters (as CHARMM is a huge force
field, sometimes things get missed and I rely on this kind of feedback).
I'll add sphingomyelin in the next release.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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--
Best Regards,
Ganesh Shahane







--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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