Re: [gmx-users] Protein ligand simulation

[bharat gupta]

On Wed, Apr 20, 2016 at 12:03 PM, Terry  wrote:

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>
> Hi,
>
> If you mean you can not see the group with command `gmx make_ndx -f
> xxx.gro`, that's because you have not created one for it. Consult the
> manual for how to use make_ndx.
>
> Terry
>

Thanks Terry. I already discussed with Justin about this problem and now I
know where I was going wrong..

>
>
> On Wed, Apr 20, 2016 at 8:09 AM, bharat gupta 
> wrote:
>
> > Dear Gmx users,
> >
> > I am performing a protein-ligand simulation using gromacs latest tutorial
> > for 5.0.x version. As per the tutorial, I included the coordinates of the
> > ligand in the complex.gro file (also updated total no. of atoms after
> > adding ligand atoms) and updated the topology file (topol.top) by
> including
> > its name under the molecules sections and also included its ligand.itp
> > file. But, I am not able to find the ligand group while making an index
> > file for it. Please let me know where am I going wrong ?
> >
> > --
> > *Best Regards*
> > BM
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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Re: [gmx-users] Protein ligand simulation

[Terry]

Hi,

If you mean you can not see the group with command `gmx make_ndx -f
xxx.gro`, that's because you have not created one for it. Consult the
manual for how to use make_ndx.

Terry


On Wed, Apr 20, 2016 at 8:09 AM, bharat gupta 
wrote:

> Dear Gmx users,
>
> I am performing a protein-ligand simulation using gromacs latest tutorial
> for 5.0.x version. As per the tutorial, I included the coordinates of the
> ligand in the complex.gro file (also updated total no. of atoms after
> adding ligand atoms) and updated the topology file (topol.top) by including
> its name under the molecules sections and also included its ligand.itp
> file. But, I am not able to find the ligand group while making an index
> file for it. Please let me know where am I going wrong ?
>
> --
> *Best Regards*
> BM
> --
> 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
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] protein ligand simulation

[Justin Lemkul]

On 4/19/16 9:22 PM, bharat gupta wrote:

On Wed, Apr 20, 2016 at 10:10 AM, Justin Lemkul  wrote:




On 4/19/16 9:08 PM, bharat gupta wrote:


On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul  wrote:




On 4/19/16 9:01 PM, bharat gupta wrote:

Thanks for your prompt response.


On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul  wrote:

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On 4/19/16 8:28 PM, bharat gupta wrote:

Hi Justin,



Here's the link for following files: complex.gro, CT3.itp (ligand
topology), CT3.gro (ligand coordinates) and topology.top.



https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA=drive_web

When I run make_ndx command using the solvated complex file
(solv.gro),
I
don't find the ligand in any of the groups. Here's the output of that
command:

Command line:
  make_ndx -f solv.gro -o index.ndx


Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   368Protein residues
There are: 14227  Water residues
Analysing Protein...

  0 System  : 46221 atoms
  1 Protein :  3540 atoms
  2 Protein-H   :  2746 atoms
  3 C-alpha :   367 atoms
  4 Backbone:  1101 atoms
  5 MainChain   :  1470 atoms
  6 MainChain+Cb:  1795 atoms
  7 MainChain+H :  1826 atoms
  8 SideChain   :  1714 atoms
  9 SideChain-H :  1276 atoms
 10 Prot-Masses :  3540 atoms
 11 non-Protein : 42681 atoms
 12 Water   : 42681 atoms
 13 SOL : 42681 atoms
 14 non-Water   :  3540 atoms


Then solv.gro clearly doesn't contain your ligand; you haven't


constructed
the system properly.

I have did exactly what the tutorial mentioned about ligand topology


preparation. I have sent you the files as well (complex.gro, topol.top).
I
did this preparation at least 2-3 times but every time  I don't get the
ligand. Did you have a look at these files ??


Your problem is with solv.gro, and since none of the files provided are

solv.gro, they are not relevant.

Here's the link.

https://drive.google.com/open?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA



Apparently you added your ligand to residuetypes.dat and called it
Protein.  You have 3540 atoms that are identified as Protein by make_ndx;
that encompasses the actual protein and the ligand.  You can still select
the ligand by its residue name or number, but it won't appear in any
selection lists as a separate entry if you tell GROMACS tools to consider
it protein.  This will cause issues with some analysis tools like do_dssp
and gmx chi.


Okay, but it means that I have done something wrong while preparing the
files for the ligand. Actually, I didn't add the ligand to
residuetypes.dat, I did exactly what the protein-ligand tutorial mentioned.

Now, I got to know where the error is. I should rename my ligand instead of
using CT3. As, CT3 is already present in the residuetypes.dat file.
Atlast, after spending 2 horrible days at this, I can move forward with the
simulation.

Regarding the ligand parameters after optimization (from ATB server), I
already checked the post you mentioned earlier. But, my doubt is whether is
it reasonable to use the unoptimized ligand for simulation ??



Force fields with a strong connection to QM always start by deriving parameters 
from the optimized geometry.  For GROMOS, where the parametrization is done very 
empirically, I don't how important this will be.  You can, of course, generate 
two topologies and compare them.  What you should *not* do is use the optimized 
geometry as it has been minimized in vacuo and therefore no longer is likely to 
have any resemblance to the structure that is bound to your protein.  For a 
trisaccharide, which is very flexible, this is particularly important.



Also, I am using gromacs v 5.0.4 and I want to use the tool g_puckering
which was written for v 4.x.x. I am not able to compile that, so could you
recommend so other tool to calculate cremer pople parameters for sugar
puckering, as my ligand is a trisaccharide ?



If nothing else, it's all derived from simple geometric measurements that can be 
made using GROMACS utilities.


-Justin

--

Re: [gmx-users] protein ligand simulation

[bharat gupta]

On Wed, Apr 20, 2016 at 10:10 AM, Justin Lemkul  wrote:

>
>
> On 4/19/16 9:08 PM, bharat gupta wrote:
>
>> On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 4/19/16 9:01 PM, bharat gupta wrote:
>>>
>>> Thanks for your prompt response.

 On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul  wrote:

 [image: Boxbe]  This message is
 eligible

> for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule
> <
>
> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DnqH3v%252FMS7bSEnB454b3Ikkoit6nvnpvzcrlHpGyN%252FWIOKBoecFU4zltFf7D%252FYHe8BMrH1ORmgTsP4gtx3fq3yEa336uM2rOLjzwPj4EjjwW0R0s7UGq4mdNAYkzXlGsJnrJrUQmI2jI%253D%26key%3DaZka6hEojvmt2tNDVLAPxoi7nhM7mRhpdu5MiY96JP8%253D_serial=25130648872_rand=1182875792_source=stf_medium=email_campaign=ANNO_CLEANUP_ADD_content=001
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>>
>> | More info
> <
>
> http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=25130648872_rand=1182875792_source=stf_medium=email_campaign=ANNO_CLEANUP_ADD_content=001
>
>>
>>
>
>
>
> On 4/19/16 8:28 PM, bharat gupta wrote:
>
> Hi Justin,
>
>>
>> Here's the link for following files: complex.gro, CT3.itp (ligand
>> topology), CT3.gro (ligand coordinates) and topology.top.
>>
>>
>>
>> https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA=drive_web
>>
>> When I run make_ndx command using the solvated complex file
>> (solv.gro),
>> I
>> don't find the ligand in any of the groups. Here's the output of that
>> command:
>>
>> Command line:
>>  make_ndx -f solv.gro -o index.ndx
>>
>>
>> Reading structure file
>> Going to read 0 old index file(s)
>> Analysing residue names:
>> There are:   368Protein residues
>> There are: 14227  Water residues
>> Analysing Protein...
>>
>>  0 System  : 46221 atoms
>>  1 Protein :  3540 atoms
>>  2 Protein-H   :  2746 atoms
>>  3 C-alpha :   367 atoms
>>  4 Backbone:  1101 atoms
>>  5 MainChain   :  1470 atoms
>>  6 MainChain+Cb:  1795 atoms
>>  7 MainChain+H :  1826 atoms
>>  8 SideChain   :  1714 atoms
>>  9 SideChain-H :  1276 atoms
>> 10 Prot-Masses :  3540 atoms
>> 11 non-Protein : 42681 atoms
>> 12 Water   : 42681 atoms
>> 13 SOL : 42681 atoms
>> 14 non-Water   :  3540 atoms
>>
>>
>> Then solv.gro clearly doesn't contain your ligand; you haven't
>>
> constructed
> the system properly.
>
> I have did exactly what the tutorial mentioned about ligand topology
>
 preparation. I have sent you the files as well (complex.gro, topol.top).
 I
 did this preparation at least 2-3 times but every time  I don't get the
 ligand. Did you have a look at these files ??


 Your problem is with solv.gro, and since none of the files provided are
>>> solv.gro, they are not relevant.
>>>
>>> Here's the link.
>> https://drive.google.com/open?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA
>>
>>
> Apparently you added your ligand to residuetypes.dat and called it
> Protein.  You have 3540 atoms that are identified as Protein by make_ndx;
> that encompasses the actual protein and the ligand.  You can still select
> the ligand by its residue name or number, but it won't appear in any
> selection lists as a separate entry if you tell GROMACS tools to consider
> it protein.  This will cause issues with some analysis tools like do_dssp
> and gmx chi.

Okay, but it means that I have done something wrong while preparing the
files for the ligand. Actually, I didn't add the ligand to
residuetypes.dat, I did exactly what the protein-ligand tutorial mentioned.

Now, I got to know where the error is. I should rename my ligand instead of
using CT3. As, CT3 is already present in the residuetypes.dat file.
Atlast, after spending 2 horrible days at this, I can move forward with the
simulation.

Regarding the ligand parameters after optimization (from ATB server), I
already checked the post you mentioned earlier. But, my doubt is whether is
it reasonable to use the unoptimized ligand for simulation ??

Also, I am using gromacs v 5.0.4 and I want to use the tool g_puckering
which was written for v 4.x.x. I am not able to compile that, so could you
recommend so other tool to calculate cremer pople parameters for sugar
puckering, as my ligand is a trisaccharide ?

Thanks Justin


>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of 

[gmx-users] The reproduction of Barnase-Barstar binding energy

[Paris Tzou]

Dear all,

I am trying to reproduce the Barnase-Barstar binding energy  published
in 2010 in Biopolymers entitled "Downhill Binding Energy Surface of the
Barnase–Barstar Complex"   by using Umbrella sampling introduced in the
Gromacs tutorial page
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html


I follow the parameter setup found in the paper but the binding energy
is around 210 KJoul instead of 40 KJoul. That's a big difference. Since the
affinity constant of Barnase-Barstar is known, this test of reproduction is
important in proving Umbrella Sampling can be used to estimate the binding
energy.

Does anybody have any suggestion ?

Thanks a lot for your time,

Paris

 
  Paris Tzou
  Department of Bioscience and Biotechnology
  National Taiwan Ocean University
  2, Pei-Ning Road, Keelung, Taiwan 20224, R. O. C.
  Office: 886-2-2462 2192 ext  5522
  Fax: 886-2-2462 2320
  Cellular: 0928 305 905
  E-mail: parist...@gmail.com
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Re: [gmx-users] protein ligand simulation

[Justin Lemkul]

On 4/19/16 9:08 PM, bharat gupta wrote:

On Wed, Apr 20, 2016 at 10:05 AM, Justin Lemkul  wrote:




On 4/19/16 9:01 PM, bharat gupta wrote:


Thanks for your prompt response.

On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul  wrote:

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On 4/19/16 8:28 PM, bharat gupta wrote:

Hi Justin,


Here's the link for following files: complex.gro, CT3.itp (ligand
topology), CT3.gro (ligand coordinates) and topology.top.


https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA=drive_web

When I run make_ndx command using the solvated complex file (solv.gro),
I
don't find the ligand in any of the groups. Here's the output of that
command:

Command line:
 make_ndx -f solv.gro -o index.ndx


Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   368Protein residues
There are: 14227  Water residues
Analysing Protein...

 0 System  : 46221 atoms
 1 Protein :  3540 atoms
 2 Protein-H   :  2746 atoms
 3 C-alpha :   367 atoms
 4 Backbone:  1101 atoms
 5 MainChain   :  1470 atoms
 6 MainChain+Cb:  1795 atoms
 7 MainChain+H :  1826 atoms
 8 SideChain   :  1714 atoms
 9 SideChain-H :  1276 atoms
10 Prot-Masses :  3540 atoms
11 non-Protein : 42681 atoms
12 Water   : 42681 atoms
13 SOL : 42681 atoms
14 non-Water   :  3540 atoms


Then solv.gro clearly doesn't contain your ligand; you haven't

constructed
the system properly.

I have did exactly what the tutorial mentioned about ligand topology

preparation. I have sent you the files as well (complex.gro, topol.top).
I
did this preparation at least 2-3 times but every time  I don't get the
ligand. Did you have a look at these files ??



Your problem is with solv.gro, and since none of the files provided are
solv.gro, they are not relevant.


Here's the link.
https://drive.google.com/open?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA



Apparently you added your ligand to residuetypes.dat and called it Protein.  You 
have 3540 atoms that are identified as Protein by make_ndx; that encompasses the 
actual protein and the ligand.  You can still select the ligand by its residue 
name or number, but it won't appear in any selection lists as a separate entry 
if you tell GROMACS tools to consider it protein.  This will cause issues with 
some analysis tools like do_dssp and gmx chi.


-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] protein ligand simulation

[Justin Lemkul]

On 4/19/16 9:01 PM, bharat gupta wrote:

Thanks for your prompt response.

On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul  wrote:


[image: Boxbe]  This message is eligible
for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule

| More info




On 4/19/16 8:28 PM, bharat gupta wrote:


Hi Justin,

Here's the link for following files: complex.gro, CT3.itp (ligand
topology), CT3.gro (ligand coordinates) and topology.top.

https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA=drive_web

When I run make_ndx command using the solvated complex file (solv.gro), I
don't find the ligand in any of the groups. Here's the output of that
command:

Command line:
make_ndx -f solv.gro -o index.ndx


Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   368Protein residues
There are: 14227  Water residues
Analysing Protein...

0 System  : 46221 atoms
1 Protein :  3540 atoms
2 Protein-H   :  2746 atoms
3 C-alpha :   367 atoms
4 Backbone:  1101 atoms
5 MainChain   :  1470 atoms
6 MainChain+Cb:  1795 atoms
7 MainChain+H :  1826 atoms
8 SideChain   :  1714 atoms
9 SideChain-H :  1276 atoms
   10 Prot-Masses :  3540 atoms
   11 non-Protein : 42681 atoms
   12 Water   : 42681 atoms
   13 SOL : 42681 atoms
   14 non-Water   :  3540 atoms



Then solv.gro clearly doesn't contain your ligand; you haven't constructed
the system properly.


I have did exactly what the tutorial mentioned about ligand topology
preparation. I have sent you the files as well (complex.gro, topol.top).  I
did this preparation at least 2-3 times but every time  I don't get the
ligand. Did you have a look at these files ??



Your problem is with solv.gro, and since none of the files provided are 
solv.gro, they are not relevant.


-Justin



Also, when I ran pdb2gmx command for my protein, I got two files :

porse_Protein_chainA.itp and chainA2.itp. Does that mean somewhere the
protein chain is broken in the initial structure?



This just means you have multiple chains.

For, my ligand I generated the parameters using ATB server, but the problem

is that when I used the optimized geometry and itp files for the ligand,
it's located far away from the active site. So, should I used the
unoptimized geometry coordinates in that case, but wouldn't it be wrong to
use the unoptimized geometry??



Do not optimize the geometry; you need the ligand's bound state to avoid
such problems.  This issue came up in another thread just a few hours ago
(it pays to read others' posts - quite often you'll learn something :)

-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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--
==

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] protein ligand simulation

[bharat gupta]

Thanks for your prompt response.

On Wed, Apr 20, 2016 at 9:31 AM, Justin Lemkul  wrote:

> [image: Boxbe]  This message is eligible
> for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule
> 
> | More info
> 
>
>
>
> On 4/19/16 8:28 PM, bharat gupta wrote:
>
>> Hi Justin,
>>
>> Here's the link for following files: complex.gro, CT3.itp (ligand
>> topology), CT3.gro (ligand coordinates) and topology.top.
>>
>> https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA=drive_web
>>
>> When I run make_ndx command using the solvated complex file (solv.gro), I
>> don't find the ligand in any of the groups. Here's the output of that
>> command:
>>
>> Command line:
>>make_ndx -f solv.gro -o index.ndx
>>
>>
>> Reading structure file
>> Going to read 0 old index file(s)
>> Analysing residue names:
>> There are:   368Protein residues
>> There are: 14227  Water residues
>> Analysing Protein...
>>
>>0 System  : 46221 atoms
>>1 Protein :  3540 atoms
>>2 Protein-H   :  2746 atoms
>>3 C-alpha :   367 atoms
>>4 Backbone:  1101 atoms
>>5 MainChain   :  1470 atoms
>>6 MainChain+Cb:  1795 atoms
>>7 MainChain+H :  1826 atoms
>>8 SideChain   :  1714 atoms
>>9 SideChain-H :  1276 atoms
>>   10 Prot-Masses :  3540 atoms
>>   11 non-Protein : 42681 atoms
>>   12 Water   : 42681 atoms
>>   13 SOL : 42681 atoms
>>   14 non-Water   :  3540 atoms
>>
>>
> Then solv.gro clearly doesn't contain your ligand; you haven't constructed
> the system properly.
>
I have did exactly what the tutorial mentioned about ligand topology
preparation. I have sent you the files as well (complex.gro, topol.top).  I
did this preparation at least 2-3 times but every time  I don't get the
ligand. Did you have a look at these files ??

>
> Also, when I ran pdb2gmx command for my protein, I got two files :
>> porse_Protein_chainA.itp and chainA2.itp. Does that mean somewhere the
>> protein chain is broken in the initial structure?
>>
>>
> This just means you have multiple chains.
>
> For, my ligand I generated the parameters using ATB server, but the problem
>> is that when I used the optimized geometry and itp files for the ligand,
>> it's located far away from the active site. So, should I used the
>> unoptimized geometry coordinates in that case, but wouldn't it be wrong to
>> use the unoptimized geometry??
>>
>>
> Do not optimize the geometry; you need the ligand's bound state to avoid
> such problems.  This issue came up in another thread just a few hours ago
> (it pays to read others' posts - quite often you'll learn something :)
>
> -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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Bharat
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Re: [gmx-users] protein ligand simulation

[Justin Lemkul]

On 4/19/16 8:28 PM, bharat gupta wrote:

Hi Justin,

Here's the link for following files: complex.gro, CT3.itp (ligand
topology), CT3.gro (ligand coordinates) and topology.top.
https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA=drive_web

When I run make_ndx command using the solvated complex file (solv.gro), I
don't find the ligand in any of the groups. Here's the output of that
command:

Command line:
   make_ndx -f solv.gro -o index.ndx


Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   368Protein residues
There are: 14227  Water residues
Analysing Protein...

   0 System  : 46221 atoms
   1 Protein :  3540 atoms
   2 Protein-H   :  2746 atoms
   3 C-alpha :   367 atoms
   4 Backbone:  1101 atoms
   5 MainChain   :  1470 atoms
   6 MainChain+Cb:  1795 atoms
   7 MainChain+H :  1826 atoms
   8 SideChain   :  1714 atoms
   9 SideChain-H :  1276 atoms
  10 Prot-Masses :  3540 atoms
  11 non-Protein : 42681 atoms
  12 Water   : 42681 atoms
  13 SOL : 42681 atoms
  14 non-Water   :  3540 atoms



Then solv.gro clearly doesn't contain your ligand; you haven't constructed the 
system properly.



Also, when I ran pdb2gmx command for my protein, I got two files :
porse_Protein_chainA.itp and chainA2.itp. Does that mean somewhere the
protein chain is broken in the initial structure?



This just means you have multiple chains.


For, my ligand I generated the parameters using ATB server, but the problem
is that when I used the optimized geometry and itp files for the ligand,
it's located far away from the active site. So, should I used the
unoptimized geometry coordinates in that case, but wouldn't it be wrong to
use the unoptimized geometry??



Do not optimize the geometry; you need the ligand's bound state to avoid such 
problems.  This issue came up in another thread just a few hours ago (it pays to 
read others' posts - quite often you'll learn something :)


-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] protein ligand simulation

[bharat gupta]

Hi Justin,

Here's the link for following files: complex.gro, CT3.itp (ligand
topology), CT3.gro (ligand coordinates) and topology.top.
https://drive.google.com/folderview?id=0B6ehLXK0eP7sa0NSZ1A0QjhTcDA=drive_web

When I run make_ndx command using the solvated complex file (solv.gro), I
don't find the ligand in any of the groups. Here's the output of that
command:

Command line:
  make_ndx -f solv.gro -o index.ndx


Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:   368Protein residues
There are: 14227  Water residues
Analysing Protein...

  0 System  : 46221 atoms
  1 Protein :  3540 atoms
  2 Protein-H   :  2746 atoms
  3 C-alpha :   367 atoms
  4 Backbone:  1101 atoms
  5 MainChain   :  1470 atoms
  6 MainChain+Cb:  1795 atoms
  7 MainChain+H :  1826 atoms
  8 SideChain   :  1714 atoms
  9 SideChain-H :  1276 atoms
 10 Prot-Masses :  3540 atoms
 11 non-Protein : 42681 atoms
 12 Water   : 42681 atoms
 13 SOL : 42681 atoms
 14 non-Water   :  3540 atoms

Also, when I ran pdb2gmx command for my protein, I got two files :
porse_Protein_chainA.itp and chainA2.itp. Does that mean somewhere the
protein chain is broken in the initial structure?

For, my ligand I generated the parameters using ATB server, but the problem
is that when I used the optimized geometry and itp files for the ligand,
it's located far away from the active site. So, should I used the
unoptimized geometry coordinates in that case, but wouldn't it be wrong to
use the unoptimized geometry??

Thanks

--
BM


On Tue, Apr 19, 2016 at 10:08 PM, Justin Lemkul  wrote:

>
>
> On 4/19/16 9:03 AM, bharat gupta wrote:
>
>> Dear Gmx users,
>>
>> I am performing a protein-ligand simulation using gromacs latest tutorial
>> for 5.0.x version. As per the tutorial, I included the coordinates of the
>> ligand in the complex.gro file (also updated total no. of atoms after
>> adding ligand atoms) and updated the topology file (topol.top) by
>> including
>> its name under the molecules sections and also included its ligand.itp
>> file. But, I am not able to find the ligand group while making an index
>> file for it. Please let me know where am I going wrong ?
>>
>>
> Well the ligand can't suddenly disappear, but in the absence of your
> actual commands and the screen output of make_ndx, there's nothing anyone
> can conclude about what the issue is.
>
> -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] Protein ligand simulation

[bharat gupta]

Dear Gmx users,

I am performing a protein-ligand simulation using gromacs latest tutorial
for 5.0.x version. As per the tutorial, I included the coordinates of the
ligand in the complex.gro file (also updated total no. of atoms after
adding ligand atoms) and updated the topology file (topol.top) by including
its name under the molecules sections and also included its ligand.itp
file. But, I am not able to find the ligand group while making an index
file for it. Please let me know where am I going wrong ?

-- 
*Best Regards*
BM
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Re: [gmx-users] estimated density while using solvate

[Mark Abraham]

Hi,

share/top/atommass.dat allows GROMACS tools to guess masses from atom names

Mark

On Tue, Apr 19, 2016 at 4:53 PM Irem Altan  wrote:

> Hi,
>
> When I use gmx solvate, it prints out an estimated density. Is it possible
> to know how this value is calculated? How is the solvent volume estimated?
>
> Best,
> Irem
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Re: [gmx-users] Adapting metallic ions from AMBER to GROMACS

[Pedro Lacerda]

Very thanks,

I'm trying it right now.

Pedro Lacerda

2016-04-18 21:29 GMT-03:00 Mark Abraham :

> Hi,
>
> Convert the units and absorb the factor of two to the minus six. Compare
> with other ions present in both representations of such force fields.
>
> Mark
>
> On Tue, 19 Apr 2016 02:21 Pedro Lacerda  wrote:
>
> > Hi Gromacs users,
> >
> > We are planning a simulation with a metallic (fe+2) attached on the
> > protein. The parameters found in [1] cannot be directly inserted on
> > ffnonbonded.itp because equation 1 of [1] and equation 4.5 of [2] are
> > slightly different.
> >
> > Theoreticaly these Lennard-Jones parameters could be used in any PME
> based
> > force field, but it was derived and tested using the AMBER software and
> > potential, so it is our current force field of choice. In
> > amber99sb-ildn/ffnonbonded.itp the long range interactions are described
> in
> > terms of epsilon (kJ/mol) and sigma (Rmin; nm).
> >
> > Eq 1:
> >
> > Lj = 4e ((R/r)^12 - (R/r)^6)
> >
> > Eq 4.5:
> >
> > Lj = e ((R/r)^12 - 2(R/r)^6)
> >
> > Seems that Rmin values are written as Rmin/2 in AMBER files avoiding some
> > calculations to optimize the software. But this occurs at implementation
> > level and probably does not have correspondence with the paper.
> >
> > My question is how can I adapt these parameters so they can be used in
> > Gromacs?
> >
> > (Sorry about the previous email, now the title is correct)
> >
> > [1]
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728907/pdf/nihms481931.pdf
> >
> > [2] ftp://ftp.gromacs.org/pub/manual/manual-5.1.2.pdf
> >
> > [3] http://comments.gmane.org/gmane.science.biology.gromacs.user/82242
> >
> >
> > Cheers,
> >
> > Pedro Lacerda
> > --
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Re: [gmx-users] Zn moves away from protein - ligand complex

[Mark Abraham]

Hi,

You've already said you know the ion isn't diffusing out, so there can be
no simulation problem.

You'd have the same kind of visualisation problem if the default protein
index group didn't exist and instead each residue was its own group. Then
they would each be handled separately, and thus not necessarily
consistently with each other. If you want a whole assembly treated
together, you have to ask for it explicitly. The protein has a default
index group to do that, because people normally want that. Currently only
you know that this ion is special, so the computer can't know that you
care...

Mark

On Tue, 19 Apr 2016 04:13 HongTham  wrote:

> Hi Mark,
> Sorry that I don't get you. Can you explain a little bit for me? I just
> wonder if Zn really moves out of active site, when I display multi box in
> VMD, there shouldn't have another Zn bound in there.
> Sincerely,
> Hongtham
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Re: [gmx-users] SETTLE vs. LINCS -- different final energies of energy minimized structures

[Mark Abraham]

Hi,


On Tue, Apr 19, 2016 at 4:49 PM Rakesh Sharan  wrote:

> Thanks Justin and Mark!
>
> I am sorry for not being clear. Actually I am taking configurations from an
> equilibrated MD trajectory and minimizing these configuration using two
> constraints -- LINCS and SETTLE. So, basically my initial starting
> configuration is exactly same for each minimization (using SETTLE and
> LINCS), but in few cases final energy of the minimized configurations are
> different (in one case its -29146 and -29288 kj/mol) depending on the
> choice of constraint algorithm used.
>
> During energy minimization, for few configurations, in case of SETTLE I am
> getting warning "Water molecule starting at atom 1893 can not be settled"
> and in case of LINCS 4-5 warnings like "bonds that rotated more than 30
> degrees" (runs are not crashing).
>

That sounds like your actual workflow isn't what you think it is.
Equilibrated snapshots of rigid water recorded at pretty much any precision
should do EM smoothly and cleanly.

Mark, actually I am interested in the structural features of energy
> minimized (or inherent) structures. This is the reason that I want to make
> sure that I have properly energy minimized structures.
>

But "proper" doesn't have a clear meaning. If there was a single global
minimum and a smooth hypersurface then you would expect multiple
algorithms, etc. to achieve numerically the same result. But this system
has a lot of roughness, many similar minima, and there is no reason to
expect the algorithms to produce the same result, nor anything you could
deduce about the one that they found. Any single EM run is as "proper" as
you could hope for.

Mark


> Best,
> Rakesh
>
> 
> Rakesh S. Singh, Ph.D.
> Postdoctoral Research Associate,
> Department of Chemical & Biological Engineering,
> Princeton University,
> Princeton, NJ 08544 (US).
>
>
> On Mon, Apr 18, 2016 at 12:24 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > I would further speculate that these differences are not even
> significant.
> > You can also try rotating the whole system with gmx editconf before you
> > generate the EM input, and that will be enough to change the order of
> the
> > floating point arithmetic, so that a different final energy minimum will
> be
> > found. I don't know offhand what range of energy values you might expect,
> > but you already have some related data for that, from your multiple EM
> runs
> > from different starting points.
> >
> > I'm also sceptical about whether anything useful can be observed; the
> > potential energy surface is only somewhat relevant to the properties of
> the
> > thermalized ensemble.
> >
> > Mark
> >
> > On Mon, 18 Apr 2016 18:12 Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 4/18/16 10:30 AM, Rakesh Sharan wrote:
> > > > Thanks very much Justin.
> > > >
> > > > Actually I am minimization a series of configurations from an
> > > equilibrated
> > > > trajectory of bulk TIP4P/2005 (LINCS used as constraint algorithm). I
> > > need
> > >
> > > So, to be clear, you altered the TIP4P topology to use a system of 3
> > > constraints
> > > that were held rigid by LINCS, using "constraints = all-bonds" when
> doing
> > > the
> > > simulation?  Simply setting LINCS as the constraint method in the .mdp
> > > file is
> > > insufficient to turn off SETTLE (which is always used unless you tell
> > > mdrun not to).
> > >
> > > > the final energy of the energy minimized structures, however, you can
> > see
> > > > that depending on the choice of constrained algorithm, for few
> > > > configurations, the final energy is different (e. g. for the attached
> > > plot
> > > > -29146 and -29288 kj/mol). Actually, both are following same
> > minimization
> > >
> > > The list doesn't allow attachments.
> > >
> > > Re-minimizing a configuration with different algorithms may lead to
> some
> > > differences, I would suspect.  But the internal geometry should be the
> > > same, so
> > > all that's varying will be LJ and electrostatic terms.  You can check
> by
> > > doing a
> > > further decomposition into which term is changing the most.
> > >
> > > > trajectory, however, one is finishing before other. This is bit
> > troubling
> > > > as depending on the choice of constraint algorithm average final
> energy
> > > is
> > > > different even though initial starting configuration is exactly
> same. I
> > > > rechecked topology files and they look same apart from constraint
> > > > specifications.
> > > >
> > >
> > > So let me clarify, because I'm not sure if I follow what you're saying
> > > (because
> > > here it sounds like you're talking about running different simulations,
> > > whereas
> > > above it sounds like a very different case).  Which is true:
> > >
> > > 1. You are doing two simulations from the same starting configuration
> and
> > > are
> > > trying to compare the final energy.
> > > 2. You are 

Re: [gmx-users] MARTINI simulation of protein-protein recognition

[jkrieger]

ok shouldn't martinize do the equivalent to pdb2gmx, i.e. make the final
pdb or gro file and a corresponding topology? Your problem is with genbox
with thinks MEMBRANEsystem.gro is the solvent and therefore will not be
connected like protein and membrane. My suggestion to take the placements
from genbox but remake the pdb can presumably still be done to make input
for martinize just like it could for pdb2gmx.

Best wishes
James

> no pdb2gmx will not work because I am working with the martini CG models
>
> how I fix the issue it reorent the atom names by hands (coppy protein
> and lipids from the initial pdbs which were submitted to genbox to the
> complex.gro because initially I had properly oriented complexes).
>
> BTW where I can find smth useful regarding mdp options for the system
> which include 2 unbound protein comlexes. E.g how it better to define
> coupling groups for the barostat and thermostat assuming that 1
> proteis is inserted within the membrane and another is within the
> water.
>
> Thanks!!!
>
> J.
>
> 2016-04-19 15:54 GMT+02:00  :
>> How about aligning the original MEMBRANEsystem.gro and waterSOLprot.gro
>> onto the relevant part of solvatedNEW.gro in pymol (after converting to
>> PDB) and then creating and saving a new object from both parts which you
>> use as input for pdb2gmx to create the topology. That way both parts
>> have
>> their original residue orders.
>>
>>> a now I understand that genbox has reorented the order the residues in
>>> the protein which was embedded in the membrane used as the solvent >)
>>>
>>> is it possible to prevent the order of all residues in the system
>>> provided by -cs flag?
>>>
>>> 2016-04-19 15:14 GMT+02:00 James Starlight :
 btw I have tried to insert second molecular using just genbox having
 both components oriented properly in the space before

 g_genbox -cp waterSOLprot.gro -cs MEMBRANEsystem.gro -vdwd 0.21 -o
 solvatedNEW.gro -box 18 18 28

 than checking VMD solvatedNEW.gro - everything was looks perfect- the
 waterSOLprot has been placed in proper position and overlapped CG
 water has been removed.

 now running gromppt I received

 WARNING 1 [file system.top, line 49]:
   2886 non-matching atom names
   atom names from system.top will be used
   atom names from system.gro will be ignored


 I also should specify that after genbox I edited new topology.top
 manually
 putting chains of the proteins in correct order (like in new gro file
 produced by genbox) and putting correct number of W

 assuming that initially I have multi chain protein in the POPC
 membrane
 and using genbox I added to the system one new chain Z

 before
 [quote]Protein_A  1
 Protein_B  1
 Protein_C  1
 Protein_D  1
 Protein_E  1
 Protein_F  1
 Protein_G  1
 Protein_H  1
 Protein_I  1
 Protein_J  1
 Protein_K  1
 Protein_L  1
 Protein_M  1
 POPC   451
 CHOL 0
 POPC   451
 CHOL 0
 W61226
 NA+678
 CL-671[/quote]

 after
 [quote]Protein_Z  1
 Protein_A  1
 Protein_B  1
 Protein_C  1
 Protein_D  1
 Protein_E  1
 Protein_F  1
 Protein_G  1
 Protein_H  1
 Protein_I  1
 Protein_J  1
 Protein_K  1
 Protein_L  1
 Protein_M  1
 POPC   451
 CHOL 0
 POPC   451
 CHOL 0
 W60817
 NA+678
 CL-671[/quote]

 where I did mistake? Does genbox reorent atom order in the -cp
 waterSOLprot.gro -cs MEMBRANEsystem.gro ? Could it be fixed?

 2016-04-18 16:21 GMT+02:00 James Starlight :
> Ok thanks I will look into the tutorial!
>
> J.
>
> 2016-04-18 16:02 GMT+02:00 Kroon, P.C. :
>> @Michael: Yes, you are right, a protein is a protein. IIRC the
>> martinize
>> script does the same as pdb2gmx in this case.
>> @James: It really sounds like you want to do DAFT.
>> http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
>> seems to contain an tutorial. Otherwise, consider contacting the
>> author of
>> the paper (T Wassenaar).
>>
>> Peter
>>
>> On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D.
>> 
>> wrote:
>>
>>> Hi James,
>>>
>>> My guess is that running a two (unbound) protein simulation with
>>> the
>>> MARTINI force-field will be the same as if it was all atom. Build
>>> two
>>> separate protein topologies (with Martini force-fields) as *.itp
>>> files to
>>> include in your *.top and 

Re: [gmx-users] SETTLE vs. LINCS -- different final energies of energy minimized structures

[Rakesh Sharan]

Thanks Justin and Mark!

I am sorry for not being clear. Actually I am taking configurations from an
equilibrated MD trajectory and minimizing these configuration using two
constraints -- LINCS and SETTLE. So, basically my initial starting
configuration is exactly same for each minimization (using SETTLE and
LINCS), but in few cases final energy of the minimized configurations are
different (in one case its -29146 and -29288 kj/mol) depending on the
choice of constraint algorithm used.

During energy minimization, for few configurations, in case of SETTLE I am
getting warning "Water molecule starting at atom 1893 can not be settled"
and in case of LINCS 4-5 warnings like "bonds that rotated more than 30
degrees" (runs are not crashing).

Mark, actually I am interested in the structural features of energy
minimized (or inherent) structures. This is the reason that I want to make
sure that I have properly energy minimized structures.

Best,
Rakesh


Rakesh S. Singh, Ph.D.
Postdoctoral Research Associate,
Department of Chemical & Biological Engineering,
Princeton University,
Princeton, NJ 08544 (US).


On Mon, Apr 18, 2016 at 12:24 PM, Mark Abraham 
wrote:

> Hi,
>
> I would further speculate that these differences are not even significant.
> You can also try rotating the whole system with gmx editconf before you
> generate the EM input, and that will be enough to change the order of  the
> floating point arithmetic, so that a different final energy minimum will be
> found. I don't know offhand what range of energy values you might expect,
> but you already have some related data for that, from your multiple EM runs
> from different starting points.
>
> I'm also sceptical about whether anything useful can be observed; the
> potential energy surface is only somewhat relevant to the properties of the
> thermalized ensemble.
>
> Mark
>
> On Mon, 18 Apr 2016 18:12 Justin Lemkul  wrote:
>
> >
> >
> > On 4/18/16 10:30 AM, Rakesh Sharan wrote:
> > > Thanks very much Justin.
> > >
> > > Actually I am minimization a series of configurations from an
> > equilibrated
> > > trajectory of bulk TIP4P/2005 (LINCS used as constraint algorithm). I
> > need
> >
> > So, to be clear, you altered the TIP4P topology to use a system of 3
> > constraints
> > that were held rigid by LINCS, using "constraints = all-bonds" when doing
> > the
> > simulation?  Simply setting LINCS as the constraint method in the .mdp
> > file is
> > insufficient to turn off SETTLE (which is always used unless you tell
> > mdrun not to).
> >
> > > the final energy of the energy minimized structures, however, you can
> see
> > > that depending on the choice of constrained algorithm, for few
> > > configurations, the final energy is different (e. g. for the attached
> > plot
> > > -29146 and -29288 kj/mol). Actually, both are following same
> minimization
> >
> > The list doesn't allow attachments.
> >
> > Re-minimizing a configuration with different algorithms may lead to some
> > differences, I would suspect.  But the internal geometry should be the
> > same, so
> > all that's varying will be LJ and electrostatic terms.  You can check by
> > doing a
> > further decomposition into which term is changing the most.
> >
> > > trajectory, however, one is finishing before other. This is bit
> troubling
> > > as depending on the choice of constraint algorithm average final energy
> > is
> > > different even though initial starting configuration is exactly same. I
> > > rechecked topology files and they look same apart from constraint
> > > specifications.
> > >
> >
> > So let me clarify, because I'm not sure if I follow what you're saying
> > (because
> > here it sounds like you're talking about running different simulations,
> > whereas
> > above it sounds like a very different case).  Which is true:
> >
> > 1. You are doing two simulations from the same starting configuration and
> > are
> > trying to compare the final energy.
> > 2. You are re-minimizing each frame of an existing trajectory and
> comparing
> > energies.
> >
> > #1 really doesn't make sense, as all MD simulations are chaotic, and I'm
> > not
> > sure what #2 would achieve.
> >
> > > I would very much appreciate your view over the plausible origin of
> this
> > > discrepancy. Also, I am wondering whether in both the cases one is
> doing
> > > truly constrained minimization.
> > >
> >
> > If there are no bond or angle energy values, the waters were constrained.
> >
> > -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
> > 

[gmx-users] estimated density while using solvate

[Irem Altan]

Hi,

When I use gmx solvate, it prints out an estimated density. Is it possible to 
know how this value is calculated? How is the solvent volume estimated?

Best,
Irem
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Re: [gmx-users] position restrain energy

[Justin Lemkul]

On 4/19/16 9:57 AM, Nikhil Maroli wrote:

reference previous mail thread :
https://www.mail-archive.com/gromacs.org_gmx-users%40maillist.sys.kth.se/msg18799.html

Dear Justin,
Thanks ,so i have to define restrain for individual molecules.in that case
how should i define *mdp file ,since eight restrains are there for each
ring A,B,C,D,E,F,G,H .
in mpd define  = -DPOSRES   what name i will give here,



If you have multiple #ifdef keywords, you need a series of define statements, 
e.g.

define = -DPOSRES_PROTA -DPOSRES_PROTB...

If the restraints are all meant to be on at the same time, then just put each 
restraint file within an #ifdef POSRES ... #endif block.  Having separate 
keywords is only necessary if you need some restraints on while others are off.


-Justin



topology looks like

#include "toppar/PROA.itp"
#ifdef POSRES_PROTA
#include "posre_cpn.itp"
#endif

#include "toppar/PROB.itp"
#ifdef POSRES_PROTB
#include "posre_cpn.itp"
#endif
#include "toppar/PROC.itp"
#ifdef POSRES_PROTC
#include "posre_cpn.itp"
#endif
#include "toppar/PROD.itp"
#ifdef POSRES_PROTD
#include "posre_cpn.itp"
#endif
#include "toppar/PROE.itp"
#ifdef POSRES_PROTE
#include "posre_cpn.itp"
#endif
#include "toppar/PROF.itp"
#ifdef POSRES_PROTF
#include "posre_cpn.itp"
#endif
#include "toppar/PROG.itp"
#ifdef POSRES_PROTG
#include "posre_cpn.itp"
#endif


#include "toppar/PROH.itp"




--
==

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] MARTINI simulation of protein-protein recognition

[James Starlight]

no pdb2gmx will not work because I am working with the martini CG models

how I fix the issue it reorent the atom names by hands (coppy protein
and lipids from the initial pdbs which were submitted to genbox to the
complex.gro because initially I had properly oriented complexes).

BTW where I can find smth useful regarding mdp options for the system
which include 2 unbound protein comlexes. E.g how it better to define
coupling groups for the barostat and thermostat assuming that 1
proteis is inserted within the membrane and another is within the
water.

Thanks!!!

J.

2016-04-19 15:54 GMT+02:00  :
> How about aligning the original MEMBRANEsystem.gro and waterSOLprot.gro
> onto the relevant part of solvatedNEW.gro in pymol (after converting to
> PDB) and then creating and saving a new object from both parts which you
> use as input for pdb2gmx to create the topology. That way both parts have
> their original residue orders.
>
>> a now I understand that genbox has reorented the order the residues in
>> the protein which was embedded in the membrane used as the solvent >)
>>
>> is it possible to prevent the order of all residues in the system
>> provided by -cs flag?
>>
>> 2016-04-19 15:14 GMT+02:00 James Starlight :
>>> btw I have tried to insert second molecular using just genbox having
>>> both components oriented properly in the space before
>>>
>>> g_genbox -cp waterSOLprot.gro -cs MEMBRANEsystem.gro -vdwd 0.21 -o
>>> solvatedNEW.gro -box 18 18 28
>>>
>>> than checking VMD solvatedNEW.gro - everything was looks perfect- the
>>> waterSOLprot has been placed in proper position and overlapped CG
>>> water has been removed.
>>>
>>> now running gromppt I received
>>>
>>> WARNING 1 [file system.top, line 49]:
>>>   2886 non-matching atom names
>>>   atom names from system.top will be used
>>>   atom names from system.gro will be ignored
>>>
>>>
>>> I also should specify that after genbox I edited new topology.top
>>> manually
>>> putting chains of the proteins in correct order (like in new gro file
>>> produced by genbox) and putting correct number of W
>>>
>>> assuming that initially I have multi chain protein in the POPC membrane
>>> and using genbox I added to the system one new chain Z
>>>
>>> before
>>> [quote]Protein_A  1
>>> Protein_B  1
>>> Protein_C  1
>>> Protein_D  1
>>> Protein_E  1
>>> Protein_F  1
>>> Protein_G  1
>>> Protein_H  1
>>> Protein_I  1
>>> Protein_J  1
>>> Protein_K  1
>>> Protein_L  1
>>> Protein_M  1
>>> POPC   451
>>> CHOL 0
>>> POPC   451
>>> CHOL 0
>>> W61226
>>> NA+678
>>> CL-671[/quote]
>>>
>>> after
>>> [quote]Protein_Z  1
>>> Protein_A  1
>>> Protein_B  1
>>> Protein_C  1
>>> Protein_D  1
>>> Protein_E  1
>>> Protein_F  1
>>> Protein_G  1
>>> Protein_H  1
>>> Protein_I  1
>>> Protein_J  1
>>> Protein_K  1
>>> Protein_L  1
>>> Protein_M  1
>>> POPC   451
>>> CHOL 0
>>> POPC   451
>>> CHOL 0
>>> W60817
>>> NA+678
>>> CL-671[/quote]
>>>
>>> where I did mistake? Does genbox reorent atom order in the -cp
>>> waterSOLprot.gro -cs MEMBRANEsystem.gro ? Could it be fixed?
>>>
>>> 2016-04-18 16:21 GMT+02:00 James Starlight :
 Ok thanks I will look into the tutorial!

 J.

 2016-04-18 16:02 GMT+02:00 Kroon, P.C. :
> @Michael: Yes, you are right, a protein is a protein. IIRC the
> martinize
> script does the same as pdb2gmx in this case.
> @James: It really sounds like you want to do DAFT.
> http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
> seems to contain an tutorial. Otherwise, consider contacting the
> author of
> the paper (T Wassenaar).
>
> Peter
>
> On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D. 
> wrote:
>
>> Hi James,
>>
>> My guess is that running a two (unbound) protein simulation with the
>> MARTINI force-field will be the same as if it was all atom. Build two
>> separate protein topologies (with Martini force-fields) as *.itp
>> files to
>> include in your *.top and go from there. The topology file is what
>> grompp
>> uses to determine bonding, so if the topology file doesn't have the
>> two
>> proteins bound, they won't be. If I remember correctly, you can see
>> an
>> example (all-atom) topology file to work with if you use pdb2gmx for
>> a pdb
>> that contains 2 chains (with the proper flag the chains will be
>> split).
>>
>> -Micholas
>>
>> ===
>> Micholas Dean Smith, PhD.
>> Post-doctoral Research Associate
>> University of Tennessee/Oak Ridge National Laboratory
>> Center 

Re: [gmx-users] position restrain energy

[Nikhil Maroli]

reference previous mail thread :
https://www.mail-archive.com/gromacs.org_gmx-users%40maillist.sys.kth.se/msg18799.html

Dear Justin,
Thanks ,so i have to define restrain for individual molecules.in that case
how should i define *mdp file ,since eight restrains are there for each
ring A,B,C,D,E,F,G,H .
in mpd define  = -DPOSRES   what name i will give here,


topology looks like

#include "toppar/PROA.itp"
#ifdef POSRES_PROTA
#include "posre_cpn.itp"
#endif

#include "toppar/PROB.itp"
#ifdef POSRES_PROTB
#include "posre_cpn.itp"
#endif
#include "toppar/PROC.itp"
#ifdef POSRES_PROTC
#include "posre_cpn.itp"
#endif
#include "toppar/PROD.itp"
#ifdef POSRES_PROTD
#include "posre_cpn.itp"
#endif
#include "toppar/PROE.itp"
#ifdef POSRES_PROTE
#include "posre_cpn.itp"
#endif
#include "toppar/PROF.itp"
#ifdef POSRES_PROTF
#include "posre_cpn.itp"
#endif
#include "toppar/PROG.itp"
#ifdef POSRES_PROTG
#include "posre_cpn.itp"
#endif


#include "toppar/PROH.itp"


-- 
Ragards,
Nikhil Maroli
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Re: [gmx-users] MARTINI simulation of protein-protein recognition

[jkrieger]

How about aligning the original MEMBRANEsystem.gro and waterSOLprot.gro
onto the relevant part of solvatedNEW.gro in pymol (after converting to
PDB) and then creating and saving a new object from both parts which you
use as input for pdb2gmx to create the topology. That way both parts have
their original residue orders.

> a now I understand that genbox has reorented the order the residues in
> the protein which was embedded in the membrane used as the solvent >)
>
> is it possible to prevent the order of all residues in the system
> provided by -cs flag?
>
> 2016-04-19 15:14 GMT+02:00 James Starlight :
>> btw I have tried to insert second molecular using just genbox having
>> both components oriented properly in the space before
>>
>> g_genbox -cp waterSOLprot.gro -cs MEMBRANEsystem.gro -vdwd 0.21 -o
>> solvatedNEW.gro -box 18 18 28
>>
>> than checking VMD solvatedNEW.gro - everything was looks perfect- the
>> waterSOLprot has been placed in proper position and overlapped CG
>> water has been removed.
>>
>> now running gromppt I received
>>
>> WARNING 1 [file system.top, line 49]:
>>   2886 non-matching atom names
>>   atom names from system.top will be used
>>   atom names from system.gro will be ignored
>>
>>
>> I also should specify that after genbox I edited new topology.top
>> manually
>> putting chains of the proteins in correct order (like in new gro file
>> produced by genbox) and putting correct number of W
>>
>> assuming that initially I have multi chain protein in the POPC membrane
>> and using genbox I added to the system one new chain Z
>>
>> before
>> [quote]Protein_A  1
>> Protein_B  1
>> Protein_C  1
>> Protein_D  1
>> Protein_E  1
>> Protein_F  1
>> Protein_G  1
>> Protein_H  1
>> Protein_I  1
>> Protein_J  1
>> Protein_K  1
>> Protein_L  1
>> Protein_M  1
>> POPC   451
>> CHOL 0
>> POPC   451
>> CHOL 0
>> W61226
>> NA+678
>> CL-671[/quote]
>>
>> after
>> [quote]Protein_Z  1
>> Protein_A  1
>> Protein_B  1
>> Protein_C  1
>> Protein_D  1
>> Protein_E  1
>> Protein_F  1
>> Protein_G  1
>> Protein_H  1
>> Protein_I  1
>> Protein_J  1
>> Protein_K  1
>> Protein_L  1
>> Protein_M  1
>> POPC   451
>> CHOL 0
>> POPC   451
>> CHOL 0
>> W60817
>> NA+678
>> CL-671[/quote]
>>
>> where I did mistake? Does genbox reorent atom order in the -cp
>> waterSOLprot.gro -cs MEMBRANEsystem.gro ? Could it be fixed?
>>
>> 2016-04-18 16:21 GMT+02:00 James Starlight :
>>> Ok thanks I will look into the tutorial!
>>>
>>> J.
>>>
>>> 2016-04-18 16:02 GMT+02:00 Kroon, P.C. :
 @Michael: Yes, you are right, a protein is a protein. IIRC the
 martinize
 script does the same as pdb2gmx in this case.
 @James: It really sounds like you want to do DAFT.
 http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
 seems to contain an tutorial. Otherwise, consider contacting the
 author of
 the paper (T Wassenaar).

 Peter

 On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D. 
 wrote:

> Hi James,
>
> My guess is that running a two (unbound) protein simulation with the
> MARTINI force-field will be the same as if it was all atom. Build two
> separate protein topologies (with Martini force-fields) as *.itp
> files to
> include in your *.top and go from there. The topology file is what
> grompp
> uses to determine bonding, so if the topology file doesn't have the
> two
> proteins bound, they won't be. If I remember correctly, you can see
> an
> example (all-atom) topology file to work with if you use pdb2gmx for
> a pdb
> that contains 2 chains (with the proper flag the chains will be
> split).
>
> -Micholas
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of James
> Starlight 
> Sent: Monday, April 18, 2016 9:43 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] MARTINI simulation of protein-protein
> recognition
>
> It seems like smth very complicated :)
>
> I just need to put two different proteins in the system - one in the
> membrane (A) and one in the water (B) and simulate it independently
> 10
> times to collect statistics about associations of A and B during
> those
> runs. The problems that I don't 

Re: [gmx-users] MARTINI simulation of protein-protein recognition

[James Starlight]

a now I understand that genbox has reorented the order the residues in
the protein which was embedded in the membrane used as the solvent >)

is it possible to prevent the order of all residues in the system
provided by -cs flag?

2016-04-19 15:14 GMT+02:00 James Starlight :
> btw I have tried to insert second molecular using just genbox having
> both components oriented properly in the space before
>
> g_genbox -cp waterSOLprot.gro -cs MEMBRANEsystem.gro -vdwd 0.21 -o
> solvatedNEW.gro -box 18 18 28
>
> than checking VMD solvatedNEW.gro - everything was looks perfect- the
> waterSOLprot has been placed in proper position and overlapped CG
> water has been removed.
>
> now running gromppt I received
>
> WARNING 1 [file system.top, line 49]:
>   2886 non-matching atom names
>   atom names from system.top will be used
>   atom names from system.gro will be ignored
>
>
> I also should specify that after genbox I edited new topology.top manually
> putting chains of the proteins in correct order (like in new gro file
> produced by genbox) and putting correct number of W
>
> assuming that initially I have multi chain protein in the POPC membrane
> and using genbox I added to the system one new chain Z
>
> before
> [quote]Protein_A  1
> Protein_B  1
> Protein_C  1
> Protein_D  1
> Protein_E  1
> Protein_F  1
> Protein_G  1
> Protein_H  1
> Protein_I  1
> Protein_J  1
> Protein_K  1
> Protein_L  1
> Protein_M  1
> POPC   451
> CHOL 0
> POPC   451
> CHOL 0
> W61226
> NA+678
> CL-671[/quote]
>
> after
> [quote]Protein_Z  1
> Protein_A  1
> Protein_B  1
> Protein_C  1
> Protein_D  1
> Protein_E  1
> Protein_F  1
> Protein_G  1
> Protein_H  1
> Protein_I  1
> Protein_J  1
> Protein_K  1
> Protein_L  1
> Protein_M  1
> POPC   451
> CHOL 0
> POPC   451
> CHOL 0
> W60817
> NA+678
> CL-671[/quote]
>
> where I did mistake? Does genbox reorent atom order in the -cp
> waterSOLprot.gro -cs MEMBRANEsystem.gro ? Could it be fixed?
>
> 2016-04-18 16:21 GMT+02:00 James Starlight :
>> Ok thanks I will look into the tutorial!
>>
>> J.
>>
>> 2016-04-18 16:02 GMT+02:00 Kroon, P.C. :
>>> @Michael: Yes, you are right, a protein is a protein. IIRC the martinize
>>> script does the same as pdb2gmx in this case.
>>> @James: It really sounds like you want to do DAFT.
>>> http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
>>> seems to contain an tutorial. Otherwise, consider contacting the author of
>>> the paper (T Wassenaar).
>>>
>>> Peter
>>>
>>> On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D. 
>>> wrote:
>>>
 Hi James,

 My guess is that running a two (unbound) protein simulation with the
 MARTINI force-field will be the same as if it was all atom. Build two
 separate protein topologies (with Martini force-fields) as *.itp files to
 include in your *.top and go from there. The topology file is what grompp
 uses to determine bonding, so if the topology file doesn't have the two
 proteins bound, they won't be. If I remember correctly, you can see an
 example (all-atom) topology file to work with if you use pdb2gmx for a pdb
 that contains 2 chains (with the proper flag the chains will be split).

 -Micholas

 ===
 Micholas Dean Smith, PhD.
 Post-doctoral Research Associate
 University of Tennessee/Oak Ridge National Laboratory
 Center for Molecular Biophysics

 
 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
 gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of James
 Starlight 
 Sent: Monday, April 18, 2016 9:43 AM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] MARTINI simulation of protein-protein recognition

 It seems like smth very complicated :)

 I just need to put two different proteins in the system - one in the
 membrane (A) and one in the water (B) and simulate it independently 10
 times to collect statistics about associations of A and B during those
 runs. The problems that I don't know how to put 2 different unbound
 proteins in the MARTINI system.

 James

 2016-04-18 9:55 GMT+02:00 Kroon, P.C. :
 > Hi,
 >
 > I assume you want to study the binding of your water soluble protein to
 > your membrane(protein). DAFT was created to do just this. DOI:
 > 10.1021/ct5010092
 >
 > Peter
 >
 > On Fri, Apr 15, 2016 at 3:37 PM, James Starlight 
 > wrote:
 >
 >> Dear Gromacs users!
 >>
 >> 

Re: [gmx-users] on md of protein-ligand

[suniba]

I believe gromacs will not "find out" the bindig site, neither the servers. You 
have to make it sure. And ATB gives 56A3 and 54A7 files; any of Gromos ff 
parameters can be interconverted with slight minor modifications. For other 
ffs, very good servers are specified by Justin in his tutorial. 
Best wishes
Suniba

Sent from my iPhone

> On 19-Apr-2016, at 5:43 pm, Justin Lemkul  wrote:
> 
> 
> 
>> On 4/19/16 8:10 AM, Brett wrote:
>> Dear All,
>> 
>> 
>> It seems the external servers preparing the ligand files (antechamber for 
>> example) not only optimize the coordinates of the ligands, but it changes 
>> the ligand from one place to another place, thus the ligand coordinates by 
>> the external server cannot occupy the ligand binding pocket in the original 
>> protein-ligand complex.
>> 
>> 
>> I am looking forward to getting a reply from you on how to have the external 
>> server processed ligand find the ligand binding pocket in the protein-ligand 
>> complex for md.
> 
> Topology-generating servers aren't going to "find the ligand binding pocket" 
> - your job is to make sure the original coordinates are preserved, as the 
> previous message has instructed you on how to do.
> 
> -Justin
> 
>> 
>> Brett
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> At 2016-04-19 19:44:23, "suniba"  wrote:
>>> After pdb2gmx, protein topology is prepared. You prepare the ligand 
>>> topology from an external server or parametrize it. Then you prepare 
>>> complex.gro and include the ligand topology manually in topol.top (topology 
>>> generated by pdb2gmx). And for your second question, I used ATB today and 
>>> realized that one should always use "original geometry" co-ordinates as 
>>> 'optimized geometry' will/may cause clashes with protein etc.. So, avoid 
>>> PRODRG server and use ATB and then download the co-ordinates and .itp of 
>>> original geometry. Rest process is same as mentioned in tutorial.
>>> Regards
>>> 
>>> Sent from my iPhone
>>> 
 On 19-Apr-2016, at 4:58 pm, Brett  wrote:
 
 Dear All,
 
 
 I am learning the md of protein-ligand based on the Justin on-line 
 tutorial. My first question is, for the topology files we need to produce 
 the protein part and ligand part separately, and the input for pdb2gmx did 
 not contain the ligand part. After I got the ligand files, I find the 
 coordinate of the ligands was different from the ligand pdb in the 
 protein-complex pdb (although the rmsd between the ligand topology and the 
 ligand in the complex was 0). Then during md process how does GROMCS know 
 where is the position of the ligand in the complex?
 
 
 Correspondingly, my second question is, suppose I have a protein dimer 
 with 2 identical subunits, 1 subunit was a cAMP binding, and 1 was apo. 
 Then during the md process how does GROMACS know which subunit binding 
 with the cAMP and which subunit was apo?
 
 
 I am looking forward to getting a reply from you.
 
 
 Brett
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> ==
> 
> 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] MARTINI simulation of protein-protein recognition

[James Starlight]

btw I have tried to insert second molecular using just genbox having
both components oriented properly in the space before

g_genbox -cp waterSOLprot.gro -cs MEMBRANEsystem.gro -vdwd 0.21 -o
solvatedNEW.gro -box 18 18 28

than checking VMD solvatedNEW.gro - everything was looks perfect- the
waterSOLprot has been placed in proper position and overlapped CG
water has been removed.

now running gromppt I received

WARNING 1 [file system.top, line 49]:
  2886 non-matching atom names
  atom names from system.top will be used
  atom names from system.gro will be ignored


I also should specify that after genbox I edited new topology.top manually
putting chains of the proteins in correct order (like in new gro file
produced by genbox) and putting correct number of W

assuming that initially I have multi chain protein in the POPC membrane
and using genbox I added to the system one new chain Z

before
[quote]Protein_A  1
Protein_B  1
Protein_C  1
Protein_D  1
Protein_E  1
Protein_F  1
Protein_G  1
Protein_H  1
Protein_I  1
Protein_J  1
Protein_K  1
Protein_L  1
Protein_M  1
POPC   451
CHOL 0
POPC   451
CHOL 0
W61226
NA+678
CL-671[/quote]

after
[quote]Protein_Z  1
Protein_A  1
Protein_B  1
Protein_C  1
Protein_D  1
Protein_E  1
Protein_F  1
Protein_G  1
Protein_H  1
Protein_I  1
Protein_J  1
Protein_K  1
Protein_L  1
Protein_M  1
POPC   451
CHOL 0
POPC   451
CHOL 0
W60817
NA+678
CL-671[/quote]

where I did mistake? Does genbox reorent atom order in the -cp
waterSOLprot.gro -cs MEMBRANEsystem.gro ? Could it be fixed?

2016-04-18 16:21 GMT+02:00 James Starlight :
> Ok thanks I will look into the tutorial!
>
> J.
>
> 2016-04-18 16:02 GMT+02:00 Kroon, P.C. :
>> @Michael: Yes, you are right, a protein is a protein. IIRC the martinize
>> script does the same as pdb2gmx in this case.
>> @James: It really sounds like you want to do DAFT.
>> http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
>> seems to contain an tutorial. Otherwise, consider contacting the author of
>> the paper (T Wassenaar).
>>
>> Peter
>>
>> On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D. 
>> wrote:
>>
>>> Hi James,
>>>
>>> My guess is that running a two (unbound) protein simulation with the
>>> MARTINI force-field will be the same as if it was all atom. Build two
>>> separate protein topologies (with Martini force-fields) as *.itp files to
>>> include in your *.top and go from there. The topology file is what grompp
>>> uses to determine bonding, so if the topology file doesn't have the two
>>> proteins bound, they won't be. If I remember correctly, you can see an
>>> example (all-atom) topology file to work with if you use pdb2gmx for a pdb
>>> that contains 2 chains (with the proper flag the chains will be split).
>>>
>>> -Micholas
>>>
>>> ===
>>> Micholas Dean Smith, PhD.
>>> Post-doctoral Research Associate
>>> University of Tennessee/Oak Ridge National Laboratory
>>> Center for Molecular Biophysics
>>>
>>> 
>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of James
>>> Starlight 
>>> Sent: Monday, April 18, 2016 9:43 AM
>>> To: Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] MARTINI simulation of protein-protein recognition
>>>
>>> It seems like smth very complicated :)
>>>
>>> I just need to put two different proteins in the system - one in the
>>> membrane (A) and one in the water (B) and simulate it independently 10
>>> times to collect statistics about associations of A and B during those
>>> runs. The problems that I don't know how to put 2 different unbound
>>> proteins in the MARTINI system.
>>>
>>> James
>>>
>>> 2016-04-18 9:55 GMT+02:00 Kroon, P.C. :
>>> > Hi,
>>> >
>>> > I assume you want to study the binding of your water soluble protein to
>>> > your membrane(protein). DAFT was created to do just this. DOI:
>>> > 10.1021/ct5010092
>>> >
>>> > Peter
>>> >
>>> > On Fri, Apr 15, 2016 at 3:37 PM, James Starlight >> >
>>> > wrote:
>>> >
>>> >> Dear Gromacs users!
>>> >>
>>> >> I am looking for some tutorial for the MARTINI simulation of
>>> >> protein-protein recognition dealing with the big membrane protein
>>> >> simulated within the membrane and its assosiation with the small water
>>> >> soluble protein. The question - is it possible in existing Martini
>>> >> system conisdted of only membrane protein solvated in membrane with
>>> >> water to
>>> >> i) increase box size on Z
>>> >> ii)add some water
>>> >> iii) put another water soluble protein in new space (on the 

Re: [gmx-users] protein ligand simulation

[Justin Lemkul]

On 4/19/16 9:03 AM, bharat gupta wrote:

Dear Gmx users,

I am performing a protein-ligand simulation using gromacs latest tutorial
for 5.0.x version. As per the tutorial, I included the coordinates of the
ligand in the complex.gro file (also updated total no. of atoms after
adding ligand atoms) and updated the topology file (topol.top) by including
its name under the molecules sections and also included its ligand.itp
file. But, I am not able to find the ligand group while making an index
file for it. Please let me know where am I going wrong ?



Well the ligand can't suddenly disappear, but in the absence of your actual 
commands and the screen output of make_ndx, there's nothing anyone can conclude 
about what the issue is.


-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] semi-permeable wall in gromacs

[Justin Lemkul]

On 4/19/16 9:06 AM, gozde ergin wrote:

Is refcoord_scaling the issue for also NVT simulation?


No, it only applies when pressure coupling is applied.


Because Roux and Luo did NVT after equilibrate the system in semiisoptropic NPT.



The information you've provided (based on file names and .mdp files) suggests 
you've done this backwards; your data collection should be in NVT so the problem 
I mentioned shouldn't matter.


-Justin


On 19 Apr 2016, at 14:06, Justin Lemkul  wrote:


On 4/19/16 6:15 AM, gozde ergin wrote:

This is my posre.itp file;

[ position_restraints ]
; i  funct   gr(nm)   k
   1 252.4 4184
   2 252.4 4184

My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of 
the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 4.8-2.4=2.4nm
This step is working without any problem.

Than I use the command of;

gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy

I extract all ions z-coordinate of the ions.
Than I use the equation in Roux2010 paper in order to estimate the osmotic 
pressure which is,

 = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation only 
the ions who have passed the wall.
 = [k (1/N)sum(N) sum(i)(| zi-zwall2 |)

Fwall = (Fwall1 + Fwall2)/2
P = /Area

However I get *very* different results than Roux2010. Even though our 
temperature, non-bond settings, system size etc are the same.

Has anyone here done simulations to calculate the osmotic pressure and/or 
osmotic coefficient?
Any suggestion?


You may want to try this in CHARMM or NAMD, where it is quite honestly much 
easier.  All the specifications in GROMACS are relative to the initial 
configuration, and then there's refcoord_scaling to deal with, so I'm not 100% 
sure that this is as straightforward as it seems.  In CHARMM and NAMD, the 
positions of the walls are set explicitly and it is very straightforward to do 
these calculations.



Also Roux2010 mentioned that the force of the wall is *half harmonic* , what is 
the force in gromacs for flat-bottom restraint?



It's the same.  This just means there's a harmonic potential at the wall.  The flat-bottom 
restraint says "apply a restraint potential if z > some value" and since there's a 
second restraint that applies a force if z < some value, each restraint covers half of a 
harmonic potential.

-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] semi-permeable wall in gromacs

[gozde ergin]

Is refcoord_scaling the issue for also NVT simulation? 
Because Roux and Luo did NVT after equilibrate the system in semiisoptropic NPT.

> On 19 Apr 2016, at 14:06, Justin Lemkul  wrote:
> 
> 
> On 4/19/16 6:15 AM, gozde ergin wrote:
>> This is my posre.itp file;
>> 
>> [ position_restraints ]
>> ; i  funct   gr(nm)   k
>>   1 252.4 4184
>>   2 252.4 4184
>> 
>> My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of 
>> the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 
>> 4.8-2.4=2.4nm
>> This step is working without any problem.
>> 
>> Than I use the command of;
>> 
>> gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy
>> 
>> I extract all ions z-coordinate of the ions.
>> Than I use the equation in Roux2010 paper in order to estimate the osmotic 
>> pressure which is,
>> 
>>  = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation 
>> only the ions who have passed the wall.
>>  = [k (1/N)sum(N) sum(i)(| zi-zwall2 |)
>> 
>> Fwall = (Fwall1 + Fwall2)/2
>> P = /Area
>> 
>> However I get *very* different results than Roux2010. Even though our 
>> temperature, non-bond settings, system size etc are the same.
>> 
>> Has anyone here done simulations to calculate the osmotic pressure and/or 
>> osmotic coefficient?
>> Any suggestion?
> 
> You may want to try this in CHARMM or NAMD, where it is quite honestly much 
> easier.  All the specifications in GROMACS are relative to the initial 
> configuration, and then there's refcoord_scaling to deal with, so I'm not 
> 100% sure that this is as straightforward as it seems.  In CHARMM and NAMD, 
> the positions of the walls are set explicitly and it is very straightforward 
> to do these calculations.
> 
>> 
>> Also Roux2010 mentioned that the force of the wall is *half harmonic* , what 
>> is the force in gromacs for flat-bottom restraint?
>> 
> 
> It's the same.  This just means there's a harmonic potential at the wall.  
> The flat-bottom restraint says "apply a restraint potential if z > some 
> value" and since there's a second restraint that applies a force if z < some 
> value, each restraint covers half of a harmonic potential.
> 
> -Justin
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Re: [gmx-users] protein ligand simulation

[bharat gupta]

Dear Gmx users,

I am performing a protein-ligand simulation using gromacs latest tutorial
for 5.0.x version. As per the tutorial, I included the coordinates of the
ligand in the complex.gro file (also updated total no. of atoms after
adding ligand atoms) and updated the topology file (topol.top) by including
its name under the molecules sections and also included its ligand.itp
file. But, I am not able to find the ligand group while making an index
file for it. Please let me know where am I going wrong ?

--
BM
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[gmx-users] alchemical thermodynamic integration in gromacs 5.0 - bonded lambdas

[Oliwia Maria Szklarczyk]

Dear All,

I would like to run a free energy calculation using thermodynamic integration. 
The alchemical process I am simulating is a mutation of a alanine to a leucine 
in a protein. So I am creating new atoms and interactions. I changed the 
topology file such that new types of atoms, bonds, angles and dihedral angles 
are written at the end of the line for each atom that is mutated or that is 
appearing, in respective directive blocks. For atoms that are appearing I 
create them from dummy atoms. 

My question here is about the mdp file. I have vdw-lambdas and coul-lambdas 
vectors defined from 0 to 1 with delta_lambda = 0.05, so 21 lambda points. Do I 
also need to define the bonded-lambdas vector? I have the changes in bond types 
defined in the topology file, and I see that the bonded energy term changes 
between state A and B. 

Cheers,
Oliwia
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Re: [gmx-users] on md of protein-ligand

[Justin Lemkul]

On 4/19/16 8:10 AM, Brett wrote:

Dear All,


It seems the external servers preparing the ligand files (antechamber for 
example) not only optimize the coordinates of the ligands, but it changes the 
ligand from one place to another place, thus the ligand coordinates by the 
external server cannot occupy the ligand binding pocket in the original 
protein-ligand complex.


I am looking forward to getting a reply from you on how to have the external 
server processed ligand find the ligand binding pocket in the protein-ligand 
complex for md.



Topology-generating servers aren't going to "find the ligand binding pocket" - 
your job is to make sure the original coordinates are preserved, as the previous 
message has instructed you on how to do.


-Justin



Brett











At 2016-04-19 19:44:23, "suniba"  wrote:

After pdb2gmx, protein topology is prepared. You prepare the ligand topology from an 
external server or parametrize it. Then you prepare complex.gro and include the ligand 
topology manually in topol.top (topology generated by pdb2gmx). And for your second 
question, I used ATB today and realized that one should always use "original 
geometry" co-ordinates as 'optimized geometry' will/may cause clashes with protein 
etc.. So, avoid PRODRG server and use ATB and then download the co-ordinates and .itp of 
original geometry. Rest process is same as mentioned in tutorial.
Regards

Sent from my iPhone


On 19-Apr-2016, at 4:58 pm, Brett  wrote:

Dear All,


I am learning the md of protein-ligand based on the Justin on-line tutorial. My 
first question is, for the topology files we need to produce the protein part 
and ligand part separately, and the input for pdb2gmx did not contain the 
ligand part. After I got the ligand files, I find the coordinate of the ligands 
was different from the ligand pdb in the protein-complex pdb (although the rmsd 
between the ligand topology and the ligand in the complex was 0). Then during 
md process how does GROMCS know where is the position of the ligand in the 
complex?


Correspondingly, my second question is, suppose I have a protein dimer with 2 
identical subunits, 1 subunit was a cAMP binding, and 1 was apo. Then during 
the md process how does GROMACS know which subunit binding with the cAMP and 
which subunit was apo?


I am looking forward to getting a reply from you.


Brett
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==

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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] on md of protein-ligand

[Brett]

Dear All,


It seems the external servers preparing the ligand files (antechamber for 
example) not only optimize the coordinates of the ligands, but it changes the 
ligand from one place to another place, thus the ligand coordinates by the 
external server cannot occupy the ligand binding pocket in the original 
protein-ligand complex.


I am looking forward to getting a reply from you on how to have the external 
server processed ligand find the ligand binding pocket in the protein-ligand 
complex for md.


Brett











At 2016-04-19 19:44:23, "suniba"  wrote:
>After pdb2gmx, protein topology is prepared. You prepare the ligand topology 
>from an external server or parametrize it. Then you prepare complex.gro and 
>include the ligand topology manually in topol.top (topology generated by 
>pdb2gmx). And for your second question, I used ATB today and realized that one 
>should always use "original geometry" co-ordinates as 'optimized geometry' 
>will/may cause clashes with protein etc.. So, avoid PRODRG server and use ATB 
>and then download the co-ordinates and .itp of original geometry. Rest process 
>is same as mentioned in tutorial. 
>Regards
>
>Sent from my iPhone
>
>> On 19-Apr-2016, at 4:58 pm, Brett  wrote:
>> 
>> Dear All,
>> 
>> 
>> I am learning the md of protein-ligand based on the Justin on-line tutorial. 
>> My first question is, for the topology files we need to produce the protein 
>> part and ligand part separately, and the input for pdb2gmx did not contain 
>> the ligand part. After I got the ligand files, I find the coordinate of the 
>> ligands was different from the ligand pdb in the protein-complex pdb 
>> (although the rmsd between the ligand topology and the ligand in the complex 
>> was 0). Then during md process how does GROMCS know where is the position of 
>> the ligand in the complex?
>> 
>> 
>> Correspondingly, my second question is, suppose I have a protein dimer with 
>> 2 identical subunits, 1 subunit was a cAMP binding, and 1 was apo. Then 
>> during the md process how does GROMACS know which subunit binding with the 
>> cAMP and which subunit was apo?
>> 
>> 
>> I am looking forward to getting a reply from you.
>> 
>> 
>> Brett
>> -- 
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Re: [gmx-users] semi-permeable wall in gromacs

[Justin Lemkul]

On 4/19/16 6:15 AM, gozde ergin wrote:

This is my posre.itp file;

[ position_restraints ]
; i  funct   gr(nm)   k
   1 252.4 4184
   2 252.4 4184

My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of 
the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 4.8-2.4=2.4nm
This step is working without any problem.

Than I use the command of;

gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy

I extract all ions z-coordinate of the ions.
Than I use the equation in Roux2010 paper in order to estimate the osmotic 
pressure which is,

 = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation only 
the ions who have passed the wall.
 = [k (1/N)sum(N) sum(i)(| zi-zwall2 |)

Fwall = (Fwall1 + Fwall2)/2
P = /Area

However I get *very* different results than Roux2010. Even though our 
temperature, non-bond settings, system size etc are the same.

Has anyone here done simulations to calculate the osmotic pressure and/or 
osmotic coefficient?
Any suggestion?


You may want to try this in CHARMM or NAMD, where it is quite honestly much 
easier.  All the specifications in GROMACS are relative to the initial 
configuration, and then there's refcoord_scaling to deal with, so I'm not 100% 
sure that this is as straightforward as it seems.  In CHARMM and NAMD, the 
positions of the walls are set explicitly and it is very straightforward to do 
these calculations.




Also Roux2010 mentioned that the force of the wall is *half harmonic* , what is 
the force in gromacs for flat-bottom restraint?



It's the same.  This just means there's a harmonic potential at the wall.  The 
flat-bottom restraint says "apply a restraint potential if z > some value" and 
since there's a second restraint that applies a force if z < some value, each 
restraint covers half of a harmonic potential.


-Justin




On 07 Apr 2016, at 21:37, Justin Lemkul  wrote:



On 4/7/16 12:57 PM, gozde ergin wrote:

Hi Justin,

I just want to ask how is the r(nm) in posre.itp working?

I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the 
box.

When I write 2.4 in the r(nm) property for [position_restraints] in posre.itp, 
it seems all of the molecules that I apply flat-bottom restraint travel +/- 2.4 
nm.


This is expected.  The flat-bottom potential is established with respect to the 
reference coordinates.


But I do not want this, I would like to put a wall or force on +/-2.4 nm in z 
of the box.
Do you have any advice about this?



If you want walls at given z-values, the z-coordinate of species to which the 
restraint is applied have to be set to zero.  This coordinate file is passed to 
grompp -r as the reference point for the potential.

-Justin


Thanks in advance.



On 21 Mar 2016, at 18:37, Justin Lemkul  wrote:



On 3/21/16 1:29 PM, gozde ergin wrote:

Ok this was a silly question.
In g_energy command 5. one is flat-bottom posres force.
Sorry.



The output of g_energy is energy, not force.

But the quantity is simple to calculate.  If you have applied a flat-bottom 
restraint along z, then you just need the time series of the z-coordinates of 
the restrained particles.

F = k*(z-z0), where z0 is the position at which the flat-bottom restraint is 
active.  Since there are two walls, then you need to conditions, for +/- z0 and 
then the final sum should be divided by 2 before being divided by the area of 
the semipermeable wall.

-Justin


On 21 Mar 2016, at 17:26, gozde ergin  wrote:

Hey Justin,

I am just wondering in order to estimate the osmotic pressure I need extract 
the flat-bottom restraint force. (Force/Area = Pressure)
Do you have any idea to how to extract this force?

Thanks in advance




On 10 Mar 2016, at 15:58, Justin Lemkul  wrote:



On 3/10/16 4:44 AM, gozde ergin wrote:

Dear Justin,

Thanks for your respond, I assume there is a way to apply this restraint on 
specific molecules.
Because my system is mixed with organic and water and I would like to apply 
these forces on organic molecules not water?



So apply flat-bottom restraints to whatever the organic molecules are.  It's 
not something specific to ions.  You set the restraints in the molecule's 
topology (in its [moleculetype]), construct a reference coordinate file that 
defines some unphysical coordinates to be used as the center of the restraint, 
and that's it.  I've described the process in detail before so check the 
archive.

-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

==
--

Re: [gmx-users] Molecule not minimized and NVT failure

[suniba]

Thank you Mark and Justin, problem is solved with ATB. 
Regards

Sent from my iPhone

> On 18-Apr-2016, at 9:36 pm, Justin Lemkul  wrote:
> 
> 
> 
>> On 4/18/16 12:02 PM, suniba wrote:
>> 
>> Hello users I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0.
>> Therefore, following Justin's tutorial, I used PRODRG for ligand topolgy. I
> 
> After doing my tutorial, you should *not* be using PRODRG for topologies, for 
> the reasons mentioned in that very tutorial.
> 
>> have drawn ligand using chemdraw and minimized the structure using chem3D.
>> However, during energy minimization step in gromacs, the values converge
>> earlier after 490 steps of minimization. This means that structure is not
>> energy minimized properly. Also, during NVT, it crashes very early giving a
> 
> The number of steps has nothing to do with whether or not EM was effective.
> 
>> LINCS warning which is posted frequently in mailing list and the 'water'
>> molecule not settled error. I have gone through all the solutions and
>> according to my knowledge, the problem is with minimization. I am confused
>> now how to minimize the structure properly to avoid the error. The long bond
>> warning might also arise due to bad minimization? Any suggestions please. If
>> require I can paste the ligand co-ordinates.
> 
> Ligand coordinates will tell us nothing of use.  The topology is more 
> instructive, but in general go through: 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
> 
> If your topology is straight from PRODRG, that's suspect #1 on my list.
> 
> -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
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Re: [gmx-users] on md of protein-ligand

[suniba]

After pdb2gmx, protein topology is prepared. You prepare the ligand topology 
from an external server or parametrize it. Then you prepare complex.gro and 
include the ligand topology manually in topol.top (topology generated by 
pdb2gmx). And for your second question, I used ATB today and realized that one 
should always use "original geometry" co-ordinates as 'optimized geometry' 
will/may cause clashes with protein etc.. So, avoid PRODRG server and use ATB 
and then download the co-ordinates and .itp of original geometry. Rest process 
is same as mentioned in tutorial. 
Regards

Sent from my iPhone

> On 19-Apr-2016, at 4:58 pm, Brett  wrote:
> 
> Dear All,
> 
> 
> I am learning the md of protein-ligand based on the Justin on-line tutorial. 
> My first question is, for the topology files we need to produce the protein 
> part and ligand part separately, and the input for pdb2gmx did not contain 
> the ligand part. After I got the ligand files, I find the coordinate of the 
> ligands was different from the ligand pdb in the protein-complex pdb 
> (although the rmsd between the ligand topology and the ligand in the complex 
> was 0). Then during md process how does GROMCS know where is the position of 
> the ligand in the complex?
> 
> 
> Correspondingly, my second question is, suppose I have a protein dimer with 2 
> identical subunits, 1 subunit was a cAMP binding, and 1 was apo. Then during 
> the md process how does GROMACS know which subunit binding with the cAMP and 
> which subunit was apo?
> 
> 
> I am looking forward to getting a reply from you.
> 
> 
> Brett
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[gmx-users] on md of protein-ligand

[Brett]

Dear All,


I am learning the md of protein-ligand based on the Justin on-line tutorial. My 
first question is, for the topology files we need to produce the protein part 
and ligand part separately, and the input for pdb2gmx did not contain the 
ligand part. After I got the ligand files, I find the coordinate of the ligands 
was different from the ligand pdb in the protein-complex pdb (although the rmsd 
between the ligand topology and the ligand in the complex was 0). Then during 
md process how does GROMCS know where is the position of the ligand in the 
complex?


Correspondingly, my second question is, suppose I have a protein dimer with 2 
identical subunits, 1 subunit was a cAMP binding, and 1 was apo. Then during 
the md process how does GROMACS know which subunit binding with the cAMP and 
which subunit was apo?


I am looking forward to getting a reply from you.


Brett
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Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

This is my posre.itp file;

[ position_restraints ]
; i  funct   gr(nm)   k   
  1 252.4 4184
  2 252.4 4184

My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of 
the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 4.8-2.4=2.4nm
This step is working without any problem.

Than I use the command of;

gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy

I extract all ions z-coordinate of the ions. 
Than I use the equation in Roux2010 paper in order to estimate the osmotic 
pressure which is,

 = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation only 
the ions who have passed the wall.
 = [k (1/N)sum(N) sum(i)(| zi-zwall2 |) 

Fwall = (Fwall1 + Fwall2)/2
P = /Area

However I get *very* different results than Roux2010. Even though our 
temperature, non-bond settings, system size etc are the same.

Has anyone here done simulations to calculate the osmotic pressure and/or 
osmotic coefficient?
Any suggestion?

Also Roux2010 mentioned that the force of the wall is *half harmonic* , what is 
the force in gromacs for flat-bottom restraint?


> On 07 Apr 2016, at 21:37, Justin Lemkul  wrote:
> 
> 
> 
> On 4/7/16 12:57 PM, gozde ergin wrote:
>> Hi Justin,
>> 
>> I just want to ask how is the r(nm) in posre.itp working?
>> 
>> I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the 
>> box.
>> 
>> When I write 2.4 in the r(nm) property for [position_restraints] in 
>> posre.itp, it seems all of the molecules that I apply flat-bottom restraint 
>> travel +/- 2.4 nm.
> 
> This is expected.  The flat-bottom potential is established with respect to 
> the reference coordinates.
> 
>> But I do not want this, I would like to put a wall or force on +/-2.4 nm in 
>> z of the box.
>> Do you have any advice about this?
>> 
> 
> If you want walls at given z-values, the z-coordinate of species to which the 
> restraint is applied have to be set to zero.  This coordinate file is passed 
> to grompp -r as the reference point for the potential.
> 
> -Justin
> 
>> Thanks in advance.
>> 
>> 
>>> On 21 Mar 2016, at 18:37, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> On 3/21/16 1:29 PM, gozde ergin wrote:
 Ok this was a silly question.
 In g_energy command 5. one is flat-bottom posres force.
 Sorry.
 
>>> 
>>> The output of g_energy is energy, not force.
>>> 
>>> But the quantity is simple to calculate.  If you have applied a flat-bottom 
>>> restraint along z, then you just need the time series of the z-coordinates 
>>> of the restrained particles.
>>> 
>>> F = k*(z-z0), where z0 is the position at which the flat-bottom restraint 
>>> is active.  Since there are two walls, then you need to conditions, for +/- 
>>> z0 and then the final sum should be divided by 2 before being divided by 
>>> the area of the semipermeable wall.
>>> 
>>> -Justin
>>> 
> On 21 Mar 2016, at 17:26, gozde ergin  wrote:
> 
> Hey Justin,
> 
> I am just wondering in order to estimate the osmotic pressure I need 
> extract the flat-bottom restraint force. (Force/Area = Pressure)
> Do you have any idea to how to extract this force?
> 
> Thanks in advance
> 
> 
> 
>> On 10 Mar 2016, at 15:58, Justin Lemkul  wrote:
>> 
>> 
>> 
>> On 3/10/16 4:44 AM, gozde ergin wrote:
>>> Dear Justin,
>>> 
>>> Thanks for your respond, I assume there is a way to apply this 
>>> restraint on specific molecules.
>>> Because my system is mixed with organic and water and I would like to 
>>> apply these forces on organic molecules not water?
>>> 
>> 
>> So apply flat-bottom restraints to whatever the organic molecules are.  
>> It's not something specific to ions.  You set the restraints in the 
>> molecule's topology (in its [moleculetype]), construct a reference 
>> coordinate file that defines some unphysical coordinates to be used as 
>> the center of the restraint, and that's it.  I've described the process 
>> in detail before so check the archive.
>> 
>> -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 

[gmx-users] calculate change in delta G of folding due to mutation

[Tushar Ranjan Moharana]

Hi all,
I want to calculate change in delta G of folding due to mutation. I found a
nice tutorial at:
http://www3.mpibpc.mpg.de/groups/de_groot/cecam2015/peptide_mutation/

But after completion I got  everything 0.

Calculating the integral using the trapezium rule
Integral 1 0.0  +/-0.0
  std. dev.relative deviation of
   standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
  cum. 3   cum. 4
SS1   0.00e+00   0.00e+00   0.00e+00   0.0000.000


in my .xvg file Y axis is completely 0 (X axis is time). The mutations
predicted by Rosetta showed 70 REU improvement. I think I am going
somewhere wrong.
It will be a great help if someone can help me in finding my mistake.

Thanks a lot.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hey Justin, 

These result was with Parinello-Rahman.
Here is the  setting for T and P coupling;

; Temperature coupling
tcoupl   = berendsen
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Pressure coupling is on
pcoupl  = Parrinello-Rahman   
pcoupltype  = semiisotropic 
tau_p   = 2.0 2.0 
ref_p   = 150.0 1.0 
compressibility = 0 4.5e-5
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= no   

> On 18 Apr 2016, at 15:48, Justin Lemkul  wrote:
> 
> 
> 
> On 4/18/16 4:43 AM, gozde ergin wrote:
>> In Roux study they did 10 independent 1.5 ns production simulation and I did 
>> 15 ns simulation and divided it to 10 1.5ns simulations.
>> 
>> Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
>>   Roux study 300(+/- 10  bar)
>>   Experiment 300 bar
> 
> Your fluctuation seems unreasonably low.  Is this still with Berendsen?  If 
> so, repeat it using Parrinello-Rahman for the barostat.  This result should 
> be quite reproducible when using the method described exactly in the paper.
> 
> -Justin

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[gmx-users] problem regarding cut-off and the PME grid spacing

[Tuhin Samanta]

Dear Hello Gromacs users,

My system involves water molecules in a box of 5x5x5 nm3. When I was doing
the simulation for energy minimization I  got n error message --

The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

 4 particles communicated to PME node 4 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

I have changed the cut off and grid spacing but still it's showing the
error message. I know it is the problem with the parallelization. Also I
have  gone through the user forum's discussion.  So can anyone please
suggest me how to get rid of that problem.


Thank you so much.
Best regards,
Tuhin
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