Re: [gmx-users] distance restraints between different chains

[Quyen V. Vu]

I think pulling code can solve the problem,
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#com-pulling

On Fri, Mar 20, 2020 at 12:04 PM Oscar Hernandez Alba 
wrote:

> Dear all,
>
>
>
>  I am trying to run MD with a protein with four different chains. When
> I
> convert this structure to gromacs, I have four different molecules in the
> topology file. I would like to use distance restraints between specific
> atoms of different chains. I have created the itp file with the information
> of the atoms involved in distance restraints. However, when I run the MD
> simulation with distance restraints I always get the same error message : <
> you have inserted topology section "distance_restraints" in a part
> belonging
> to a different molecule than you intended to >. Can someone help me with
> this problem ? I do not what is the exact place of the <
> distance-restraints
> > section in the topology file.
>
>
>
>  Thank you very much.
>
>
>
>  Oscar
>
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[gmx-users] distance restraints between different chains

[Oscar Hernandez Alba]

Dear all, 

 

 I am trying to run MD with a protein with four different chains. When I
convert this structure to gromacs, I have four different molecules in the
topology file. I would like to use distance restraints between specific
atoms of different chains. I have created the itp file with the information
of the atoms involved in distance restraints. However, when I run the MD
simulation with distance restraints I always get the same error message : <
you have inserted topology section "distance_restraints" in a part belonging
to a different molecule than you intended to >. Can someone help me with
this problem ? I do not what is the exact place of the < distance-restraints
> section in the topology file. 

 

 Thank you very much. 

 

 Oscar 

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[gmx-users] Distance restraints at topology file between gromacs-5.1.4 and gromacs-2018.4

[Jang, Jae W.]

Hi, Gromacs users and developers

Actually, I used distance constraint for each chain.itp file.
(for example, I added following for chainA.itp /chainB.itp/chainC.itp and so on
[distance_restraints]
;   i   j   ?   label   funct   lo  up1 up2 weight
155 17621   0   2   0   1.834174633 
2.834174633 1
174 11281   1   2   0   1.948664904 
2.948664904 1
………


It was ok for gromacs-5.1.4 for running.
But, in the gromacs-2018.4, it shows following error.
All distance restraint parameter entries in the topology should be consecutive

So, I tried to remove those distance constraint from all the itp file.
Then, it runs well at gromacs-2018.4
And, I put distance restriants to only chainA.itp.
Then, it runs well at gromacs-2018.4
And, additionally, I started to put distance restraint to chainB.itp.
It started to shows the error
All distance restraint parameter entries in the topology should be consecutive
(Maybe it means all the separated each chain distance restriants should be in 
the same file. Is it right?? )

I believe gromacs-2018.4 has changed some setting.
I searched this issue in the internet, but I found no answer.

Any suggestion would be needed (urgently).
Sincerely,
Jaewan Jang
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Re: [gmx-users] Distance restraints on two TYR OH groups so that they are together

[Vytautas Rakeviius]

I altered distance restraints according to your comment into:
[ distance_restraints ]
 195 281 1 1 1 0.4 0.44 0.48 1000Still get same issue that 195 and 281 even 
move away from each other.
Here link to all files again, hopefully it will not be distorted.
http://www.mediafire.com/file/ruaxx6nbj2qpvm6/MD_4AK0_test_pub.tar.bz2
How can I drag 195 and 281closer with distance restraints? (not necessary as 
close as 0.2 nm)

 

On Wednesday, March 15, 2017 2:54 PM, Justin Lemkul  wrote:
 

 

On 3/15/17 6:28 AM, Vytautas Rakeviius wrote:
> Hello, I try to add distance restraints on two TYR OH groups so that they are 
> together in the end like this:
>
> [ distance_restraints ]
>  195 281 1 1 1 0.2 0.22 0.24 1000
> But it does not work at least over time frame I tested, they even go further 
> away from each other.
>
> Here I share my all files:MD_4AK0_test_pub.tar.bz2

That's not a valid link.

If you're trying to keep 2 oxygen atoms at a distance of 0.2 nm, that's well 
within the (likely) repulsive wall of the LJ potential, as well as being 
repulsive from the perspective of the electrostatics.  You'll either need a 
massive biasing force to keep them close, or develop a different way to keep 
them at such a distance.  Why are you imposing this bias, and at such a short 
distance?

-Justin

> System is small and easy to run (gmx grompp -f md.mdp -c npt.gro -t npt.cpt 
> -p topol.top -o md_0_1.tpr && gmx mdrun -deffnm md_0_1)What I am doing in 
> wrong way?
>
> |
> |
> |
> |  |    |
>
>    |
>
>  |
> |
> |  |
> MD_4AK0_test_pub.tar.bz2
>  MediaFire is a simple to use free service that lets you put all your photos, 
>documents, music, and video in a si...  |  |
>
>  |
>
>  |
>
>
>

-- 
==

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] Distance restraints on two TYR OH groups so that they are together

[Justin Lemkul]

On 3/15/17 6:28 AM, Vytautas Rakeviius wrote:

Hello, I try to add distance restraints on two TYR OH groups so that they are 
together in the end like this:

[ distance_restraints ]
 195 281 1 1 1 0.2 0.22 0.24 1000
But it does not work at least over time frame I tested, they even go further 
away from each other.

Here I share my all files:MD_4AK0_test_pub.tar.bz2


That's not a valid link.

If you're trying to keep 2 oxygen atoms at a distance of 0.2 nm, that's well 
within the (likely) repulsive wall of the LJ potential, as well as being 
repulsive from the perspective of the electrostatics.  You'll either need a 
massive biasing force to keep them close, or develop a different way to keep 
them at such a distance.  Why are you imposing this bias, and at such a short 
distance?


-Justin


System is small and easy to run (gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p 
topol.top -o md_0_1.tpr && gmx mdrun -deffnm md_0_1)What I am doing in wrong 
way?

|
|
|
|   ||

   |

  |
|
|   |
MD_4AK0_test_pub.tar.bz2
 MediaFire is a simple to use free service that lets you put all your photos, 
documents, music, and video in a si...  |   |

  |

  |





--
==

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

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

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

==
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[gmx-users] Distance restraints on two TYR OH groups so that they are together

[Vytautas Rakeviius]

Hello, I try to add distance restraints on two TYR OH groups so that they are 
together in the end like this:

[ distance_restraints ]
 195 281 1 1 1 0.2 0.22 0.24 1000
But it does not work at least over time frame I tested, they even go further 
away from each other.

Here I share my all files:MD_4AK0_test_pub.tar.bz2
System is small and easy to run (gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p 
topol.top -o md_0_1.tpr && gmx mdrun -deffnm md_0_1)What I am doing in wrong 
way?
  
|  
|   
|   
|   ||

   |

  |
|  
|   |  
MD_4AK0_test_pub.tar.bz2
 MediaFire is a simple to use free service that lets you put all your photos, 
documents, music, and video in a si...  |   |

  |

  |

 
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Re: [gmx-users] distance restraints in mdp

[Justin Lemkul]

Please don't reply to the entire digest.  Copy the relevant portions and use a
proper subject line.

On 3/8/16 8:19 PM, Sana Saeed wrote:

dear Justin Lemkuli already run that without restraints, it has no problems.
even i used the gro file from the simple 5ns MD but still have these same
errors and warnings. when i set Lincs constraints to all-bonds , simulation
finishes fine but by using alchemical_analysis.py for free energies it gives
errors and warnings. (Warning: states 29 and 37 have the same energies on the
dataset.) i used 42 lambdas and about 32 states are having same energies. and
when i set constraints to h-bonds then LINCS warnings. i tried to use
different options for pressure coupling also because i read somewhere it also
affects simulation. i am quite confused where the problem is. is it possible
to send you topology file and you have a look?Thanks in advance


Now we're talking about half a million different things.  When reporting a 
problem, please keep it simple.  It's impossible for anyone on this mailing list 
to be inside your head and know what you've done.


If you want to troubleshoot distance restraints, we can do that.  But let's take 
things one at a time.  If you want to share files, please upload a tarball of 
*all* input files: coordinates, topology(ies), any relevant .mdp file(s), and a 
run script that lists all of your commands, exactly in sequence as you typed 
them.  Please do not send this information privately; share with the list so 
others can contribute (I'm frankly swamped lately and have little time to delve 
deeply into such issues but I'll try to make a little time).


-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] distance restraints in mdp

[Justin Lemkul]

On 3/7/16 10:35 PM, Sana Saeed wrote:

i am performing protein ligand binding free energy calculation MD. i have
applied distance restraint to 1 pair of atoms. now when i am running md it
gives me LINCS warnings. first i thought it is because of wrong geometry so i
changed complex, now i am doing it for Lysozyme+JZ4. but still same warning.
i am confused about the distance restraints to be introduced in mdp file.
disre = simple/ensemble? i read in manual, but still confused. i tried both
with "simple it gives me LINCS warning and with ensemble it says that this
version of gromacs doesnt support it. i am using 5.1 gromacs.


Then simplify further and make sure the system runs without restraints or 
anything else.  Just normal MD.  Start simple to avoid chasing the wrong problem.


-Justin

--
==

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

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

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

==
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[gmx-users] distance restraints in mdp

[Sana Saeed]

i am performing protein ligand binding free energy calculation MD. i have 
applied distance restraint to 1 pair of atoms. now when i am running md it 
gives me LINCS warnings. first i thought it is because of wrong geometry so i 
changed complex, now i am doing it for Lysozyme+JZ4. but still same warning. i 
am confused about the distance restraints to be introduced in mdp file. disre = 
simple/ensemble? i read in manual, but still confused. i tried both with 
"simple it gives me LINCS warning and with ensemble it says that this version 
of gromacs doesnt support it. i am using 5.1 gromacs. Sana Saeed Khan,
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Re: [gmx-users] Distance Restraints

[Diogo Vila Viçosa]

Dear Steve,

First of all you should take a look in all mdp options regarding distance
restraints:
http://manual.gromacs.org/archive/4.5/online/mdp_opt.html#nmr
I am not 100% familiar with dist res in version 4.5.4 but without
dirse=simple for example I think you will not have any distance
restraints because you will be using the default value which is disre=no
I guess.

Regarding the location of the distance restraints it can be placed after
all the parameters of your molecule. Otherwise I think grompp will give an
error.

Finally, and probably the main reason for my reply, I wonder if what you
want is a distance restraints or an actual bond between the Zn and the S
atoms (four I guess).

Diogo Vila Viçosa


Em qui, 7 de mai de 2015 às 18:58, Steve Seibold steve...@ymail.com
escreveu:

  I have a two peptide system with  my second chain B having as part of its
 topology file (and sequence) a Zinc ion. That is, the Zinc ion is literally
 part of the chain so, that when I generate my itp files using pdb2gmx I get
 topol_proteinA.itp, topol_proteinB.itp (i.e. no topol_Ion.itp)...I do this
 because the distance restraint I want is between the Zinc and its
 coordinated sulfur atoms. I believe I need the Zn and the Cys SG atoms part
 of the same molecule...here, chainB.

 I have read the distance restraint info. in the manual 4.5.4; however, I
 am still unsure about how to implement it. I have gotten to the point where
 I use genrestr to generated the  itp file having the distance restraint
 matrix. Now, when I #include this (restraint) file in the topology.top or
 in the topol_proteinB.itp, I get an error saying that the restraint file is
 in the wrong location when I use the grompp to make a tpr file.I have
 also place in disre_fc = 1000 in my mdp file
 Can someone be explicit about what  I am doing wrong...I did get the
 position restraint to work, but am having trouble here.

 Thanks, Steve



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[gmx-users] Distance Restraints

[Steve Seibold]

 I have a two peptide system with  my second chain B having as part of its 
topology file (and sequence) a Zinc ion. That is, the Zinc ion is literally 
part of the chain so, that when I generate my itp files using pdb2gmx I get 
topol_proteinA.itp, topol_proteinB.itp (i.e. no topol_Ion.itp)...I do this 
because the distance restraint I want is between the Zinc and its coordinated 
sulfur atoms. I believe I need the Zn and the Cys SG atoms part of the same 
molecule...here, chainB.

I have read the distance restraint info. in the manual 4.5.4; however, I am 
still unsure about how to implement it. I have gotten to the point where I use 
genrestr to generated the  itp file having the distance restraint matrix. Now, 
when I #include this (restraint) file in the topology.top or in the 
topol_proteinB.itp, I get an error saying that the restraint file is in the 
wrong location when I use the grompp to make a tpr file.I have also place 
in disre_fc = 1000 in my mdp file
Can someone be explicit about what  I am doing wrong...I did get the position 
restraint to work, but am having trouble here.

Thanks, Steve


 
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[gmx-users] Distance restraints

[tarak karmakar]

Dear All,
I'm trying to keep distance restraints between few atoms, and for that I
have done the following,
In the topology file, I have inserted a block specifying the details of
pairs

--
; Include forcefield parameters
#include ./amber99sb-ildn.ff/forcefield.itp

; Include chain topologies
#include Protein_chain_A.itp
#ifdef DISRES
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
  3722 3760 10 1 0.19 0.22 0.23 1.0
  3722 3765 11 1 0.19 0.22 0.23 4.184
  3723 3759 12 1 0.19 0.22 0.23 1.0
  3723 3766 12 1 0.19 0.22 0.23 1.0
#endif

#include Protein_chain_B.itp

; Include water topology
#include ./amber99sb-ildn.ff/tip3p.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include ./amber99sb-ildn.ff/ions.itp

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
SOL 24565
NA   2
---
Next in the npt.mdp file I have used the following keywords,
define  = -DDISRES
disre   = simple
disre_fc= 1000

Now, while running the simulations, after few ps the distances are
increasing by 2-3 Ang. Could anyone please suggest me something related to
this?
I went through an old discussion related to the same issue here,
http://comments.gmane.org/gmane.science.biology.gromacs.user/51387

Thanks and regards,
Tarak
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[gmx-users] Distance Restraints set for water-ion cluster in gas phase (vacuum)

[liuyong_1...@dicp.ac.cn]

Dear gromacs usres,

I want to run nvt simulation of water-ion cluster (Na+(H2O)250) in gas phase 
(vacuum) at higher temperature ( bigger than 200 K). 
But the cluster will collapse at high temperature. So the distance restraints 
is used to restraint the water molecules and the ion Na+ not to keep together 
as a cluster.
But there are so many atoms to set the distance constraint in the topology. So 
how can I set set the distance constraint in the topology easilier?
How to set the distance restraint between the atoms and center of mass of the 
water-ion cluster? 

Thank you very much!
Yong Liu



liuyong_1...@dicp.ac.cn
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Re: [gmx-users] Distance Restraints set for water-ion cluster in gas phase (vacuum)

[Justin Lemkul]

On 10/13/14 4:48 AM, liuyong_1...@dicp.ac.cn wrote:

Dear gromacs usres,

I want to run nvt simulation of water-ion cluster (Na+(H2O)250) in gas phase 
(vacuum) at higher temperature ( bigger than 200 K).
But the cluster will collapse at high temperature. So the distance restraints 
is used to restraint the water molecules and the ion Na+ not to keep together 
as a cluster.
But there are so many atoms to set the distance constraint in the topology. So 
how can I set set the distance constraint in the topology easilier?
How to set the distance restraint between the atoms and center of mass of the 
water-ion cluster?



The spherical flat-bottom potential is much easier to use in this case.  See 
manual section 4.3.2 (version 5.0).


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] Distance restraints does not work?

[Emma Ahlstrand]

Thanks Justin.

I was concerned about that the distance could increase so much above 0.4 (I
had the feeling from the equation that the penalty was larger above
up2(0.4)).  
   50.0000.4642269
  100.0000.4505744 

But anyway when I checked the interactions to Zn I found a competing
interaction with an oxygen that could play a role. When I got rid of that
and decreased up2 to 0.3 I got what I wanted.

/Emma

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