Re: [gmx-users] Homology model refinement

[Amir Zeb]

Hi Mark,

Thanks for your response. I did for simulation for both the systems 1. only
protein 2. protein with co-factor. By the way, I'm not pretty sure, but I'm
relying on rmsd of C-alpha to evaluate the structure's stability. In both
the cases, the rmsd range was highly wide ~3-6 nm. Then i superimposed the
input protein structure and the snapshot from the last frame, so the rmsd
was around 5 angstrom between the two structures.

[image: Inline image 1]

On Wed, Dec 21, 2016 at 10:27 PM, Mark Abraham 
wrote:

> Hi,
>
> On Thu, Dec 22, 2016 at 5:19 PM Amir Zeb  wrote:
>
> > Hi Mark,
> >
> > I want to refine the model for any bad contact if the structure has.
>
>
> So, do you expect the structure to be stable in the absence of the other
> things? That tells you whether you need to attempt refinement with the
> other things, or not.
>
> Mark
>
>
> > This
> > article support the simulation of any homology model after its creation
> by
> > homology modeling approach "
> > https://www.ncbi.nlm.nih.gov/pubmed/22513870?dopt=Abstract;. Do you
> please
> > think that there is no need to refine the model via simulation? or the
> > claim which i do for refinement via simulation, is biased?
> >
> > Thanks for consideration!
> >
> > Amir
> >
> > On Wed, Dec 21, 2016 at 10:09 PM, Mark Abraham  >
> > wrote:
> >
> > > Hi,
> > >
> > > What us the purpose in doing MD on the homology model? That'll tell you
> > > whether you need a model with the other parts.
> > >
> > > Mark
> > >
> > > On Thu, 22 Dec 2016 16:51 Amir Zeb  wrote:
> > >
> > > > Hello,
> > > >
> > > > I have created a homology model for a protein, where the seq.
> identity
> > > > between the template and target is 40%. The template structure also
> > > > contains co-factor and an inhibitor in bound form means it is a
> > complex.
> > > > I'll have to define the ligand binding site in target (homology
> model)
> > > > based on inhibitor bound in template structure. But before to reach
> > that
> > > > stage, i want to simulate the created model to refine the structure
> > which
> > > > is a common practice in modelling. I'm not pretty sure that should i
> > > > simulate the model structure along with the inhibitor and co-factor
> > from
> > > > template, or one of them, or just only the protein structure alone?
> > > Please
> > > > let me, if you have any referenced answer.
> > > >
> > > > Regards
> > > >
> > > > Amir
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
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Re: [gmx-users] Homology model refinement

[Mark Abraham]

Hi,

On Thu, Dec 22, 2016 at 5:19 PM Amir Zeb  wrote:

> Hi Mark,
>
> I want to refine the model for any bad contact if the structure has.


So, do you expect the structure to be stable in the absence of the other
things? That tells you whether you need to attempt refinement with the
other things, or not.

Mark


> This
> article support the simulation of any homology model after its creation by
> homology modeling approach "
> https://www.ncbi.nlm.nih.gov/pubmed/22513870?dopt=Abstract;. Do you please
> think that there is no need to refine the model via simulation? or the
> claim which i do for refinement via simulation, is biased?
>
> Thanks for consideration!
>
> Amir
>
> On Wed, Dec 21, 2016 at 10:09 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > What us the purpose in doing MD on the homology model? That'll tell you
> > whether you need a model with the other parts.
> >
> > Mark
> >
> > On Thu, 22 Dec 2016 16:51 Amir Zeb  wrote:
> >
> > > Hello,
> > >
> > > I have created a homology model for a protein, where the seq. identity
> > > between the template and target is 40%. The template structure also
> > > contains co-factor and an inhibitor in bound form means it is a
> complex.
> > > I'll have to define the ligand binding site in target (homology model)
> > > based on inhibitor bound in template structure. But before to reach
> that
> > > stage, i want to simulate the created model to refine the structure
> which
> > > is a common practice in modelling. I'm not pretty sure that should i
> > > simulate the model structure along with the inhibitor and co-factor
> from
> > > template, or one of them, or just only the protein structure alone?
> > Please
> > > let me, if you have any referenced answer.
> > >
> > > Regards
> > >
> > > Amir
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
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Re: [gmx-users] Homology model refinement

[Amir Zeb]

Hi Mark,

I want to refine the model for any bad contact if the structure has. This
article support the simulation of any homology model after its creation by
homology modeling approach "
https://www.ncbi.nlm.nih.gov/pubmed/22513870?dopt=Abstract;. Do you please
think that there is no need to refine the model via simulation? or the
claim which i do for refinement via simulation, is biased?

Thanks for consideration!

Amir

On Wed, Dec 21, 2016 at 10:09 PM, Mark Abraham 
wrote:

> Hi,
>
> What us the purpose in doing MD on the homology model? That'll tell you
> whether you need a model with the other parts.
>
> Mark
>
> On Thu, 22 Dec 2016 16:51 Amir Zeb  wrote:
>
> > Hello,
> >
> > I have created a homology model for a protein, where the seq. identity
> > between the template and target is 40%. The template structure also
> > contains co-factor and an inhibitor in bound form means it is a complex.
> > I'll have to define the ligand binding site in target (homology model)
> > based on inhibitor bound in template structure. But before to reach that
> > stage, i want to simulate the created model to refine the structure which
> > is a common practice in modelling. I'm not pretty sure that should i
> > simulate the model structure along with the inhibitor and co-factor from
> > template, or one of them, or just only the protein structure alone?
> Please
> > let me, if you have any referenced answer.
> >
> > Regards
> >
> > Amir
> > --
> > 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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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Homology model refinement

[Mark Abraham]

Hi,

What us the purpose in doing MD on the homology model? That'll tell you
whether you need a model with the other parts.

Mark

On Thu, 22 Dec 2016 16:51 Amir Zeb  wrote:

> Hello,
>
> I have created a homology model for a protein, where the seq. identity
> between the template and target is 40%. The template structure also
> contains co-factor and an inhibitor in bound form means it is a complex.
> I'll have to define the ligand binding site in target (homology model)
> based on inhibitor bound in template structure. But before to reach that
> stage, i want to simulate the created model to refine the structure which
> is a common practice in modelling. I'm not pretty sure that should i
> simulate the model structure along with the inhibitor and co-factor from
> template, or one of them, or just only the protein structure alone? Please
> let me, if you have any referenced answer.
>
> Regards
>
> Amir
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] adding new parameters to force field

[Mark Abraham]

Hi,

Sometimes. It depends exactly which functions and function types, and
whether it's part of a moleculetype. If you don't want something, don't
include it :-)

Mark

On Thu, 22 Dec 2016 10:07 Mohsen Ramezanpour 
wrote:

> Dear Gromacs users,
>
> I have a new file with both bonded and nonbonded parameters for some atom
> types in it. I want to use these new parameters for simulation and ignore
> the parameters in force field ( if there is any parameter already exist).
>
> 1) If I add the lines from each section of new file at the end of
> corresponding section at ffbonded.itp and ffnonbonded.itp files, do I still
> need to comment out all the present parameters or they will be all
> overwritten by new defined parameters?
>
> 2) How if I just #include new file after inclusion of normal force field?
> Will it overwrite previous parameters?
>
> Reading gromacs forum discussions and manual, I still was not sure of that
> (I am using gromacs versions 4 and 5).
>
>
> *From manual 5.8.3.*
> *Adding atom types*
>
> As of GROMACS version 3.1.3, atom types can be added in an extra [
> atomtypes ] section
> after the the inclusion of the normal force field. After the definition of
> the *new atom type(s)*, ad-
> ditional non-bonded and pair parameters can be defined. In pre-3.1.3
> versions of GROMACS, the
> new atom types needed to be added in the [ atomtypes ] section of the force
> field files, be-
> cause all non-bonded parameters above the last [ atomtypes ] section would
> be overwritten
> using the standard combination rules.
>
>
> Best,
> Mohsen
>
>
>
> --
> *Rewards work better than punishment ...*
> --
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Re: [gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?

[Amir Zeb]

Hello,

You may follow "
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/
"
Everything will go fine

Good luck

Amir

On Wed, Dec 21, 2016 at 8:50 PM, Adarsh V. K. 
wrote:

> Dear all,
>
> We have a 419 amino acid long protein and planned Protein-ligand complex MD
> simulation using Gromacs 5.1.4 to check.
>
>  1. What sought of MD simulation we have to perform?.
>  2. Restrain protein alone or Restrain both protein and ligand during
> simulation?.
>  3. What is the exact command for Drug positional RMSD plot?
>  4. What is the exact command for Number of Hydrogen bond plot?
>  5. What is the exact command for Other interactions between protein and
> ligand?
>  6. how to view the trajectory files? or We have to convert the frames to
> *.pdb and view in Pymol?
>
> Regards,
> Adarsh V. K.
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[gmx-users] Homology model refinement

[Amir Zeb]

Hello,

I have created a homology model for a protein, where the seq. identity
between the template and target is 40%. The template structure also
contains co-factor and an inhibitor in bound form means it is a complex.
I'll have to define the ligand binding site in target (homology model)
based on inhibitor bound in template structure. But before to reach that
stage, i want to simulate the created model to refine the structure which
is a common practice in modelling. I'm not pretty sure that should i
simulate the model structure along with the inhibitor and co-factor from
template, or one of them, or just only the protein structure alone? Please
let me, if you have any referenced answer.

Regards

Amir
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[gmx-users] Protein-Ligand Complex MD simulation: Restrain protein alone or Restrain both protein and ligand during simulation?

[Adarsh V. K.]

Dear all,

We have a 419 amino acid long protein and planned Protein-ligand complex MD
simulation using Gromacs 5.1.4 to check.

 1. What sought of MD simulation we have to perform?.
 2. Restrain protein alone or Restrain both protein and ligand during
simulation?.
 3. What is the exact command for Drug positional RMSD plot?
 4. What is the exact command for Number of Hydrogen bond plot?
 5. What is the exact command for Other interactions between protein and
ligand?
 6. how to view the trajectory files? or We have to convert the frames to
*.pdb and view in Pymol?

Regards,
Adarsh V. K.
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[gmx-users] adding new parameters to force field

[Mohsen Ramezanpour]

Dear Gromacs users,

I have a new file with both bonded and nonbonded parameters for some atom
types in it. I want to use these new parameters for simulation and ignore
the parameters in force field ( if there is any parameter already exist).

1) If I add the lines from each section of new file at the end of
corresponding section at ffbonded.itp and ffnonbonded.itp files, do I still
need to comment out all the present parameters or they will be all
overwritten by new defined parameters?

2) How if I just #include new file after inclusion of normal force field?
Will it overwrite previous parameters?

Reading gromacs forum discussions and manual, I still was not sure of that
(I am using gromacs versions 4 and 5).


*From manual 5.8.3.*
*Adding atom types*

As of GROMACS version 3.1.3, atom types can be added in an extra [
atomtypes ] section
after the the inclusion of the normal force field. After the definition of
the *new atom type(s)*, ad-
ditional non-bonded and pair parameters can be defined. In pre-3.1.3
versions of GROMACS, the
new atom types needed to be added in the [ atomtypes ] section of the force
field files, be-
cause all non-bonded parameters above the last [ atomtypes ] section would
be overwritten
using the standard combination rules.


Best,
Mohsen



-- 
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[gmx-users] Strange pressure coupling behaviour, rapid expanding box

[Kamps, M.]

Dear GMX users,

I'm experiencing difficulties with my simulation.
I have created a ionic bonded, rough surface of gold atoms (3276
atoms) in the OPLS FF, which is held together with Lennard-Jones
interactions. In the same box I've placed a C4H10 (14 atoms) molecule,
although the problem also occurs with proteins. This box is then
solved using SPCE water, although I've also tried TIP4P water.

The box size is originally 5.4x5.4x4.5 nm, and is first energy
minimized and NVT equilibrated. Up to this point the system behaves
normal and I can't see any red flags. When I then want to NPT
equilibrate the system, something strange happens. The periodic box
seems to ´explode´, since it rapidly (but constantly) expands. The
final dimensions are 5.4x5.4x24 nm after 50ps.

Analyzing the outputs of the NPT equilibrium shows some strange
things: The initial pressure starts at roughly 14000 bar and rapidly
decreases to around 3000 bar at t=5ps, after which it linearly
decreases to 2000 bar. Since the box is rapidly expanding, the volume
of the system is linearly growing, starting at roughly 160nm3 and
expanding to 850nm3 at 50ps.

I've added two screenshots, one before and one after the simulation.
I've also uploaded a screenshot of my mdp file, since it is easier to
read from an image than in here (i think).
https://s23.postimg.org/yceosj0q3/Before.png
https://s23.postimg.org/9kjceaobv/After.png
https://s24.postimg.org/xrzza3mt1/NPT_mdp.png

My system uses a semiisotrpic pcoupletype, since I want different
behaviour in xy and z direction. The reference pressure has been set
to 1 atmosphere (almost 1 bar), while the compressibility in the xy
direction is that of the material, while in the z direction it is that
of water. I only want periodic boundary conditions in the xy
directions, and both the z planes are LJ 12-6 walls. At z=0 the wall
is behaving like the same gold atoms, with the corresponding LJ
potential, while the upper wall is exerting an LJ potential of a dummy
atom (so no LJ interaction). Might this cause the error? I varied a
lot with the wall-r-linpot option, but putting in an positive,
negative or zero value does not seem to make a difference.

Are there any ideas as to what I am doing wrong? Thanks in advance,

Mark
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Re: [gmx-users] Force field for ion-carbon interaction

[Alex]

Hi Maryam,

I am not really sure what "most proper" means when it comes to MD
simulations, but I think if we're talking about vdw/electrostatics, AMBER
and OPLS-AA are very close and have been used widely in the presence of
things like CNTs and graphene... If there's any particular effect you are
unable to reproduce with those ion descriptions, that is of course a
different problem.

Hope this helps.

Alex

On Wed, Dec 21, 2016 at 12:10 PM, Maryam Kowsar 
wrote:

> Dear all
>
> What is the best and most proper force field for ions (like Na+ and Ca2+)
> and carbon structured systems interactions? I found a few papers which used
> Amber force field. Has anyone worked with or seen any papers in this
> regard?
> Thanks.
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[gmx-users] Force field for ion-carbon interaction

[Maryam Kowsar]

Dear all

What is the best and most proper force field for ions (like Na+ and Ca2+)
and carbon structured systems interactions? I found a few papers which used
Amber force field. Has anyone worked with or seen any papers in this
regard?
Thanks.
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Re: [gmx-users] Energy conservation in NVE simulations

[Justin Lemkul]

On 12/21/16 8:57 AM, Michael K. Gilson wrote:

Dear All,

Below are more details on our efforts to maximize energy conservation in NVE
runs with gromacs, while maintaining performance.  I'd appreciate advice on the
following:

1) Is this level of drift about "as good as it gets"?
2) Or, are there ways to make it even lower?
3) Are there settings we can dial back to improve speed without substantially
increasing drift?

Many thanks,
Mike Gilson

   System: The system comprises 68679 waters, one protein with 6810
   atoms, 8 sodium ions; total 75497 atoms

   The input file is below. We have deliberately turned off COM
   restraints because we are interested in how the protein moves.



Removal of net center-of-mass motion is not a COM restraint; your protein will 
diffuse fine with comm-mode = Linear.  The removal of net COM motion is to avoid 
the flying ice cube effect.  I suspect that failing to remove net COM motion is 
actually detrimental to conservation of energy.


-Justin


   As noted before, for lincs-iter=4, the energy slope is approximately
   -0.01976 kJ/mol/ps; for lincs-iter=5, the slope is approximately
   0.00991 kJ/mol/ps. Graphs of the energy for these respective
   conditions are provided here:
   https://drive.google.com/open?id=0B0zEqb9pykUWRHlqSEJTa2lwYkk
   https://drive.google.com/open?id=0B0zEqb9pykUWMWl0OEFtNGdVbzg



   MDP:

   ;DON'T POSITION RESTRAIN THE PROTEIN: NO -DPOSRES

   ;run parameters
   integrator  = md  ; leap-frog integrator
   nsteps  = 1000  ; 0.001ps * 1000 = 10 ns
   dt= 0.001; 0.001ps smaller time step for NVE
   comm-mode= None   ; let center of mass move, calculate diffusion
   constant

   ; Output control
   nstxout = 2  ; save coordinates every 0.5 ns
   nstvout = 2  ; save velocities every 0.5 ns
   nstenergy = 2 ; save energies every 0.5 ns
   nstlog  = 2  ; update log file every 0.5 ns
   energygrps= protein non-protein

   ; Bond parameters
   continuation= yes  ; starting after nvt.mdp
   constraint_algorithm= lincs ; holonomic constraints
   constraints = all-bonds   ; all bonds are constrained
   lincs_iter= 4 ; NVE requires high lincs-iter
   lincs_order = 4 ; accuracy

   ; Neighborsearching
   cutoff-scheme   = Verlet
   ns_type = grid  ; search neighboring grid cells
   nstlist   = 10; Frequency to update the neighbor list
   and long range forces
   rcoulomb  = 1.2   ; short-range electrostatic cutoff
   (in nm)
   rvdw= 1.2   ; short-range van der Waals cutoff
   (in nm)
   verlet-buffer-tolerance = 0.005; kJ/mol/ps per particle
   pbc = xyz   ; periodic boundary conditions
   DispCorr  = EnerPres  ; account for cut-off vdW scheme

   ; Electrostatics
   coulombtype = PME   ; Particle Mesh Ewald for
   long-range electrostatics
   pme_order   = 4 ; cubic interpolation
   fourierspacing   = 0.12  ; grid spacing for FFT


   ; Pressure coupling is off
   pcoupl  = no; fixed box size gives constant V

   ; Temperature coupling is off + no simluated annealing
   tcoupl  = no ; NVE conditions

   ; Velocity generation
   gen_vel = no   ; don't assign velocities: keep from
   thermalization




--
==

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] Dihedral calculations in topology

[Justin Lemkul]

On 12/21/16 6:20 AM, Mark Abraham wrote:

Hi,

pdb2gmx told you that it saw that your rtp file didn't have default
bondedtypes, so it was going to use certain values, and that means default
dihedral type 1. If you want to use the same defaults as aminoacids.rtp,
then copy them over to the rtp file you're using :-)



Which is (just for the sake of being pedantic) exactly what the linked post says 
to do.  My .rtp entries there are just the residues that are needed.  That is 
not intended or stated to be a complete .rtp file.


-Justin


Mark

On Wed, Dec 21, 2016 at 10:12 PM Kamps, M.  wrote:


Dear Mark,

Thanks for your reply!
I am replicating Polyethylene, of which the [polymer.rtp] and the
[polymer.hdb] are exactly the same as described by Justin Lemkul in
this link:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html

So, my rtp entries are:
; Terminal PE residue (chain "begin")
;C1 is -CH3
[ EthB ]
 [ atoms ]
C1opls_135   -0.180 1
   H11opls_1400.060 1
   H12opls_1400.060 1
   H13opls_1400.0601
C2opls_136   -0.120 2
   H21opls_1400.060 2
   H22opls_1400.060 2
 [ bonds ]
C1   H11
C1   H12
C1   H13
C1   C2
C2   H21
C2   H22
C2   +C1
; Terminal PE residue (chain "end")
;C2 is -CH3
[ EthE ]
 [ atoms ]
C1opls_136   -0.120 1
   H11opls_1400.060 1
   H12opls_1400.060 1
C2opls_135   -0.180 2
   H21opls_1400.060 2
   H22opls_1400.060 2
   H23opls_1400.0602
 [ bonds ]
C1   -C2
C1   H11
C1   H12
C1   C2
C2   H21
C2   H22
C2   H23

And the used hdb entries are:
EthB  2
3 4 H1 C1 C2 +C1
2 6 H2 C2 C1 +C1
EthE  2
2 6 H1 C1 C2 -C2
3 4 H2 C2 C1 -C2

The used pdb file is:
ATOM  1  C1  EthB1   0.000   0.000   0.000
ATOM  2  C2  EthB1   1.273   0.847   0.000
ATOM  3  C1  EthE1   2.546   0.000   0.000
ATOM  4  C2  EthE1   3.818   0.847   0.000

Which is a simple C4H10 molecule, composed out of two residues, with a
total of three dihedrals. The output given by grompp is:
Setting the LD random seed to -962199660
Generated 337431 of the 337431 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 337431 of the 337431 1-4 parameter combinations
ERROR 1 [file topol_polymer.itp, line 119]:
  No default Proper Dih. types
ERROR 2 [file topol_polymer.itp, line 120]:
  No default Proper Dih. types
ERROR 3 [file topol_polymer.itp, line 121]:
  No default Proper Dih. types
Where lines 119 till 121 correspond with the three dihedrals in my
topology (of the polymer).

The output of pdb2gmx is as follows:
Opening force field file ./oplsaa_polymer.ff/aminoacids.r2b
Reading C4H10.pdb...
Read 4 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 2 residues with 4 atoms

  chain  #res #atoms
  1 ' ' 2  4

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./oplsaa_polymer.ff/atomtypes.atp
Atomtype 823
Reading residue database... (oplsaa_polymer)
Opening force field file ./oplsaa_polymer.ff/Polymer.rtp
Reading .rtp file without '[ bondedtypes ]' directive,
Will proceed as if the entry was:
[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nr_exclusions
HH14  remove_dih
 1   1  1  2   0   3
   1  1

Residue 4
Sorting it all out...
Opening force field file ./oplsaa_polymer.ff/aminoacids.rtp
Residue 55
Sorting it all out...
Opening force field file ./oplsaa_polymer.ff/surface.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a
proper dihedral
Residue 62Warning: file does not end with a newline, last line:
PTPT   0.000 0
Residue 63
Sorting it all out...
Opening force field file ./oplsaa_polymer.ff/Polymer.hdb
Opening force field file ./oplsaa_polymer.ff/aminoacids.hdb
Opening force field file ./oplsaa_polymer.ff/aminoacids.n.tdb
Opening force field file ./oplsaa_polymer.ff/aminoacids.c.tdb
Processing chain 1 (4 atoms, 2 residues)
Warning: Starting residue EthB1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue EthE1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or 

Re: [gmx-users] Dihedral calculations in topology

[Kamps, M.]

Mark,

Thanks again for the swift reply! Stupid of me to miss that message! I
noticed some other code that was generated as output of pdb2gmx, which
I do not fully understand. Can you maybe explain some of it?

Processing chain 1 (4 atoms, 2 residues)
Warning: Starting residue EthB1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue EthE1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.

I understand the two warnings. To my directory I added a file
residuetypes.dat, where I specificy that (among others) EthB and EthE
(which are the ending and beginning residues of polyethylene) are
Polymer. What does the rest of this message mean? I don't understand
how I could fix this message? Or even what it wants to do, since i've
defined my own terminal residues. Is it not possible to define my own
'group'?

residuetypes.dat:
EthBPolymer
EthEPolymer

Mark
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[gmx-users] Energy conservation in NVE simulations

[Michael K. Gilson]

Dear All,

Below are more details on our efforts to maximize energy conservation in 
NVE runs with gromacs, while maintaining performance.  I'd appreciate 
advice on the following:


1) Is this level of drift about "as good as it gets"?
2) Or, are there ways to make it even lower?
3) Are there settings we can dial back to improve speed without 
substantially increasing drift?


Many thanks,
Mike Gilson

   System: The system comprises 68679 waters, one protein with 6810
   atoms, 8 sodium ions; total 75497 atoms

   The input file is below. We have deliberately turned off COM
   restraints because we are interested in how the protein moves.

   As noted before, for lincs-iter=4, the energy slope is approximately
   -0.01976 kJ/mol/ps; for lincs-iter=5, the slope is approximately
   0.00991 kJ/mol/ps. Graphs of the energy for these respective
   conditions are provided here:
   https://drive.google.com/open?id=0B0zEqb9pykUWRHlqSEJTa2lwYkk
   https://drive.google.com/open?id=0B0zEqb9pykUWMWl0OEFtNGdVbzg



   MDP:

   ;DON'T POSITION RESTRAIN THE PROTEIN: NO -DPOSRES

   ;run parameters
   integrator  = md  ; leap-frog integrator
   nsteps  = 1000  ; 0.001ps * 1000 = 10 ns
   dt= 0.001; 0.001ps smaller time step for NVE
   comm-mode= None   ; let center of mass move, calculate diffusion
   constant

   ; Output control
   nstxout = 2  ; save coordinates every 0.5 ns
   nstvout = 2  ; save velocities every 0.5 ns
   nstenergy = 2 ; save energies every 0.5 ns
   nstlog  = 2  ; update log file every 0.5 ns
   energygrps   = protein non-protein

   ; Bond parameters
   continuation= yes  ; starting after nvt.mdp
   constraint_algorithm= lincs ; holonomic constraints
   constraints = all-bonds   ; all bonds are constrained
   lincs_iter= 4 ; NVE requires high lincs-iter
   lincs_order = 4 ; accuracy

   ; Neighborsearching
   cutoff-scheme   = Verlet
   ns_type = grid  ; search neighboring grid cells
   nstlist   = 10; Frequency to update the neighbor list
   and long range forces
   rcoulomb  = 1.2   ; short-range electrostatic cutoff
   (in nm)
   rvdw= 1.2   ; short-range van der Waals cutoff
   (in nm)
   verlet-buffer-tolerance = 0.005  ; kJ/mol/ps per particle
   pbc = xyz   ; periodic boundary conditions
   DispCorr  = EnerPres  ; account for cut-off vdW scheme

   ; Electrostatics
   coulombtype = PME   ; Particle Mesh Ewald for
   long-range electrostatics
   pme_order   = 4 ; cubic interpolation
   fourierspacing   = 0.12  ; grid spacing for FFT


   ; Pressure coupling is off
   pcoupl  = no; fixed box size gives constant V

   ; Temperature coupling is off + no simluated annealing
   tcoupl  = no ; NVE conditions

   ; Velocity generation
   gen_vel = no   ; don't assign velocities: keep from
   thermalization


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Re: [gmx-users] Dihedral calculations in topology

[Mark Abraham]

Hi,

pdb2gmx told you that it saw that your rtp file didn't have default
bondedtypes, so it was going to use certain values, and that means default
dihedral type 1. If you want to use the same defaults as aminoacids.rtp,
then copy them over to the rtp file you're using :-)

Mark

On Wed, Dec 21, 2016 at 10:12 PM Kamps, M.  wrote:

> Dear Mark,
>
> Thanks for your reply!
> I am replicating Polyethylene, of which the [polymer.rtp] and the
> [polymer.hdb] are exactly the same as described by Justin Lemkul in
> this link:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html
>
> So, my rtp entries are:
> ; Terminal PE residue (chain "begin")
> ;C1 is -CH3
> [ EthB ]
>  [ atoms ]
> C1opls_135   -0.180 1
>H11opls_1400.060 1
>H12opls_1400.060 1
>H13opls_1400.0601
> C2opls_136   -0.120 2
>H21opls_1400.060 2
>H22opls_1400.060 2
>  [ bonds ]
> C1   H11
> C1   H12
> C1   H13
> C1   C2
> C2   H21
> C2   H22
> C2   +C1
> ; Terminal PE residue (chain "end")
> ;C2 is -CH3
> [ EthE ]
>  [ atoms ]
> C1opls_136   -0.120 1
>H11opls_1400.060 1
>H12opls_1400.060 1
> C2opls_135   -0.180 2
>H21opls_1400.060 2
>H22opls_1400.060 2
>H23opls_1400.0602
>  [ bonds ]
> C1   -C2
> C1   H11
> C1   H12
> C1   C2
> C2   H21
> C2   H22
> C2   H23
>
> And the used hdb entries are:
> EthB  2
> 3 4 H1 C1 C2 +C1
> 2 6 H2 C2 C1 +C1
> EthE  2
> 2 6 H1 C1 C2 -C2
> 3 4 H2 C2 C1 -C2
>
> The used pdb file is:
> ATOM  1  C1  EthB1   0.000   0.000   0.000
> ATOM  2  C2  EthB1   1.273   0.847   0.000
> ATOM  3  C1  EthE1   2.546   0.000   0.000
> ATOM  4  C2  EthE1   3.818   0.847   0.000
>
> Which is a simple C4H10 molecule, composed out of two residues, with a
> total of three dihedrals. The output given by grompp is:
> Setting the LD random seed to -962199660
> Generated 337431 of the 337431 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 337431 of the 337431 1-4 parameter combinations
> ERROR 1 [file topol_polymer.itp, line 119]:
>   No default Proper Dih. types
> ERROR 2 [file topol_polymer.itp, line 120]:
>   No default Proper Dih. types
> ERROR 3 [file topol_polymer.itp, line 121]:
>   No default Proper Dih. types
> Where lines 119 till 121 correspond with the three dihedrals in my
> topology (of the polymer).
>
> The output of pdb2gmx is as follows:
> Opening force field file ./oplsaa_polymer.ff/aminoacids.r2b
> Reading C4H10.pdb...
> Read 4 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 0 blocks of water and 2 residues with 4 atoms
>
>   chain  #res #atoms
>   1 ' ' 2  4
>
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening force field file ./oplsaa_polymer.ff/atomtypes.atp
> Atomtype 823
> Reading residue database... (oplsaa_polymer)
> Opening force field file ./oplsaa_polymer.ff/Polymer.rtp
> Reading .rtp file without '[ bondedtypes ]' directive,
> Will proceed as if the entry was:
> [ bondedtypes ]
> ; bonds  angles  dihedrals  impropers all_dihedrals nr_exclusions
> HH14  remove_dih
>  1   1  1  2   0   3
>1  1
>
> Residue 4
> Sorting it all out...
> Opening force field file ./oplsaa_polymer.ff/aminoacids.rtp
> Residue 55
> Sorting it all out...
> Opening force field file ./oplsaa_polymer.ff/surface.rtp
> Using default: not generating all possible dihedrals
> Using default: excluding 3 bonded neighbors
> Using default: generating 1,4 H--H interactions
> Using default: removing proper dihedrals found on the same bond as a
> proper dihedral
> Residue 62Warning: file does not end with a newline, last line:
> PTPT   0.000 0
> Residue 63
> Sorting it all out...
> Opening force field file ./oplsaa_polymer.ff/Polymer.hdb
> Opening force field file ./oplsaa_polymer.ff/aminoacids.hdb
> Opening force field file ./oplsaa_polymer.ff/aminoacids.n.tdb
> Opening force field file ./oplsaa_polymer.ff/aminoacids.c.tdb
> Processing chain 1 (4 atoms, 2 residues)
> Warning: Starting residue EthB1 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue EthE1 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
> Checking for duplicate atoms
> Generating any missing hydrogen atoms and/or adding termini.
> Now 

Re: [gmx-users] Dihedral calculations in topology

[Kamps, M.]

Dear Mark,

Thanks for your reply!
I am replicating Polyethylene, of which the [polymer.rtp] and the
[polymer.hdb] are exactly the same as described by Justin Lemkul in
this link: 
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html

So, my rtp entries are:
; Terminal PE residue (chain "begin")
;C1 is -CH3
[ EthB ]
 [ atoms ]
C1opls_135   -0.180 1
   H11opls_1400.060 1
   H12opls_1400.060 1
   H13opls_1400.0601
C2opls_136   -0.120 2
   H21opls_1400.060 2
   H22opls_1400.060 2
 [ bonds ]
C1   H11
C1   H12
C1   H13
C1   C2
C2   H21
C2   H22
C2   +C1
; Terminal PE residue (chain "end")
;C2 is -CH3
[ EthE ]
 [ atoms ]
C1opls_136   -0.120 1
   H11opls_1400.060 1
   H12opls_1400.060 1
C2opls_135   -0.180 2
   H21opls_1400.060 2
   H22opls_1400.060 2
   H23opls_1400.0602
 [ bonds ]
C1   -C2
C1   H11
C1   H12
C1   C2
C2   H21
C2   H22
C2   H23

And the used hdb entries are:
EthB  2
3 4 H1 C1 C2 +C1
2 6 H2 C2 C1 +C1
EthE  2
2 6 H1 C1 C2 -C2
3 4 H2 C2 C1 -C2

The used pdb file is:
ATOM  1  C1  EthB1   0.000   0.000   0.000
ATOM  2  C2  EthB1   1.273   0.847   0.000
ATOM  3  C1  EthE1   2.546   0.000   0.000
ATOM  4  C2  EthE1   3.818   0.847   0.000

Which is a simple C4H10 molecule, composed out of two residues, with a
total of three dihedrals. The output given by grompp is:
Setting the LD random seed to -962199660
Generated 337431 of the 337431 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 337431 of the 337431 1-4 parameter combinations
ERROR 1 [file topol_polymer.itp, line 119]:
  No default Proper Dih. types
ERROR 2 [file topol_polymer.itp, line 120]:
  No default Proper Dih. types
ERROR 3 [file topol_polymer.itp, line 121]:
  No default Proper Dih. types
Where lines 119 till 121 correspond with the three dihedrals in my
topology (of the polymer).

The output of pdb2gmx is as follows:
Opening force field file ./oplsaa_polymer.ff/aminoacids.r2b
Reading C4H10.pdb...
Read 4 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 2 residues with 4 atoms

  chain  #res #atoms
  1 ' ' 2  4

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./oplsaa_polymer.ff/atomtypes.atp
Atomtype 823
Reading residue database... (oplsaa_polymer)
Opening force field file ./oplsaa_polymer.ff/Polymer.rtp
Reading .rtp file without '[ bondedtypes ]' directive,
Will proceed as if the entry was:
[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nr_exclusions
HH14  remove_dih
 1   1  1  2   0   3
   1  1

Residue 4
Sorting it all out...
Opening force field file ./oplsaa_polymer.ff/aminoacids.rtp
Residue 55
Sorting it all out...
Opening force field file ./oplsaa_polymer.ff/surface.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a
proper dihedral
Residue 62Warning: file does not end with a newline, last line:
PTPT   0.000 0
Residue 63
Sorting it all out...
Opening force field file ./oplsaa_polymer.ff/Polymer.hdb
Opening force field file ./oplsaa_polymer.ff/aminoacids.hdb
Opening force field file ./oplsaa_polymer.ff/aminoacids.n.tdb
Opening force field file ./oplsaa_polymer.ff/aminoacids.c.tdb
Processing chain 1 (4 atoms, 2 residues)
Warning: Starting residue EthB1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue EthE1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 2 residues with 14 atoms
Making bonds...
Number of bonds was 14, now 13
Generating angles, dihedrals and pairs...
Before cleaning: 27 pairs
Before cleaning: 27 dihedrals
Making cmap torsions...
There are3 dihedrals,0 impropers,   24 angles
27 pairs,   13 bonds and 0 virtual sites
Total mass 58.124 a.m.u.
Total charge -0.000 e
Writing topology
Writing coordinate file...
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Re: [gmx-users] DMSO

[Mark Abraham]

Hi,

First, have you got your system working with just protein and water? And
just Protein, water and DMSO?

Mark

On Wed, Dec 21, 2016 at 3:08 AM Hoda Alibiglou 
wrote:

> Hello
>
> I am simulating a protein in mixture of water and DMSO, I madE the box
> including water and DMSO and my protein, now I should add ions by this
> command,
>
>
> gmx grompp -f ions.mdp -c dmso_D170W_solv.gro -p topol.top -o ions.tpr
>
> but, each time I get an error because the number of atoms in my
> topology file and
>
> dmso_D170W_solv.gro, are not equal, so I add in topology file SOL  and
> DMSO molecules number manually, now my error is that DMSO is unknown,
> also I used some references and according them I choosed gromos96
> forcefield for DMSO-WATER MIXTURE.
>
> may I ask you please to help me ?
>
> Best regards,
>
> Hoda
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Re: [gmx-users] Dihedral calculations in topology

[Mark Abraham]

Hi,

On Wed, Dec 21, 2016 at 9:17 PM Kamps, M.  wrote:

> Dear GMX users,
>
> I have a few questions about something I don’t fully understand. I am
> trying to work with polymers, where the basics are written by Justin
> Lemkul via this link:
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html
>
> This works up to the point where I want to use grompp, where it gives
> errors regarding the Proper Dihedral types; No default Proper Dih.
> types. When consulting the lines where these errors refers to, it is
> caused by the three dihedrals defined in my topology:
>
> [ dihedrals ]
> ;  aiajakal functc0c1
> c2c3c4c5
> 2 1 5 8 1
> 1 5 811 1
> 5 81112 1
>
> Now, according to the manual table 5.5, page 138 (v. 2016.1), these
> three dihedrals are defined as funct=1, which corresponds with a
> proper dihedral, while by default the OPLS ff only knows R-B
> dihedrals, which are funct=3. Up to this point my story is correct
> right?
>

The normal [bondedtypes] defaults in oplsaa.ff/aminoacids.rtp uses dihedral
type 3, yes. Whether that's applicable to your case we can't tell. Which
file are your .rtp entries coming from? The terminal output of pdb2gmx and
grompp say a lot of useful things about which it would be nice not to guess.

Mark

Then, why does pdb2gmx select this dihedral type? In the above
> topology [ai aj ak al] = [1 5 8 11] refers to a [opls_135 opls_136
> opls_136 opls_135] dihedral, which I believe is a [CT CT CT CT]
> dihedral. This dihedral is already defined by ffbonded.itp as follows:
>   CT CT CT CT  3  2.92880  -1.46440   0.20920
> -1.67360   0.0   0.0 ; hydrocarbon all-atom
> Am I correct about this part?
>
> Is it valid to manually change the funct=1 in the above topology to
> funct=3 to use this dihedral type? And if it is valid, how can I
> prevent pdb2gmx to assign a funct=1 to the topology?
>
> Mark
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Re: [gmx-users] Unstable Alpha Helix

[Mark Abraham]

Hi,

Yes of course lots of mdp parameters affect the quality of your model
physics. You should choose them carefully, in particular to align with how
your force field was parameterized, or is subsequently used (and shown to
work well). Offhand, the AMBER force fields are paramterized and used plain
cutoff VDW, so your use of potential-switch implements a model that is at
best doubtful until shown otherwise.

Mark

On Wed, Dec 21, 2016 at 9:16 PM  wrote:

> Hello Justin,
> I am using "stride" program to analyze the helices.
> Can the Potential switch and other mdp parameters affect the stability of
> an Alphahelix.
>
> Regards,
> Amit
> > Date: Mon, 19 Dec 2016 08:06:29 -0500
> > From: Justin Lemkul 
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Unstable Alpha Helix
> > Message-ID: <78b951a1-4cb3-e4fc-4239-cc19fd03c...@vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 12/19/16 7:01 AM, amitbe...@chemeng.iisc.ernet.in wrote:
> >> Hello everyone,
> >> I am trying to simulate an Alpha helix inside a bilayer. But a part of
> >> the
> >> alpha helix is loosing its form and converting into turns( while
> >> alphahelix should be stable in the bilayer environment)
> >
> > How are you assessing this?  DSSP?  Dihedral time series?  Note that
> > simple
> > visualization is often misleading.  Helices can still be helices, even if
> > the
> > program you're looking at disagrees.
> >
> > -Justin
> >
> >> I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer.
> >> I am using Potential-switch for VdW and PME for electrostatics.
> >> Does these parameters affect the form of the Alphahelix ?
> >>
> >> Regards,
> >> Amit
> >>
> >
> > --
> > ==
> >
> > 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] Unstable Alpha Helix

[amitbehra]

Hello Justin,
I am using "stride" program to analyze the helices.
Can the Potential switch and other mdp parameters affect the stability of
an Alphahelix.

Regards,
Amit
> Date: Mon, 19 Dec 2016 08:06:29 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Unstable Alpha Helix
> Message-ID: <78b951a1-4cb3-e4fc-4239-cc19fd03c...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/19/16 7:01 AM, amitbe...@chemeng.iisc.ernet.in wrote:
>> Hello everyone,
>> I am trying to simulate an Alpha helix inside a bilayer. But a part of
>> the
>> alpha helix is loosing its form and converting into turns( while
>> alphahelix should be stable in the bilayer environment)
>
> How are you assessing this?  DSSP?  Dihedral time series?  Note that
> simple
> visualization is often misleading.  Helices can still be helices, even if
> the
> program you're looking at disagrees.
>
> -Justin
>
>> I am using Amber-99sb-ILDN for the protein and Slipids for the bilayer.
>> I am using Potential-switch for VdW and PME for electrostatics.
>> Does these parameters affect the form of the Alphahelix ?
>>
>> Regards,
>> Amit
>>
>
> --
> ==
>
> 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] Dihedral calculations in topology

[Kamps, M.]

Dear GMX users,

I have a few questions about something I don’t fully understand. I am
trying to work with polymers, where the basics are written by Justin
Lemkul via this link:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html

This works up to the point where I want to use grompp, where it gives
errors regarding the Proper Dihedral types; No default Proper Dih.
types. When consulting the lines where these errors refers to, it is
caused by the three dihedrals defined in my topology:

[ dihedrals ]
;  aiajakal functc0c1
c2c3c4c5
2 1 5 8 1
1 5 811 1
5 81112 1

Now, according to the manual table 5.5, page 138 (v. 2016.1), these
three dihedrals are defined as funct=1, which corresponds with a
proper dihedral, while by default the OPLS ff only knows R-B
dihedrals, which are funct=3. Up to this point my story is correct
right?

Then, why does pdb2gmx select this dihedral type? In the above
topology [ai aj ak al] = [1 5 8 11] refers to a [opls_135 opls_136
opls_136 opls_135] dihedral, which I believe is a [CT CT CT CT]
dihedral. This dihedral is already defined by ffbonded.itp as follows:
  CT CT CT CT  3  2.92880  -1.46440   0.20920
-1.67360   0.0   0.0 ; hydrocarbon all-atom
Am I correct about this part?

Is it valid to manually change the funct=1 in the above topology to
funct=3 to use this dihedral type? And if it is valid, how can I
prevent pdb2gmx to assign a funct=1 to the topology?

Mark
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Re: [gmx-users] Manual refinement of ATB topologies ?

[Sim gmx]

Thank you for your reply.

I will try this and, at the same time, try to get started with CHARMM36.

About the bonded parameters, I guess I have to keep for instance the ATB
parameters for the peculiar cyclic structure, but what about let's say the
two double bonds ? I found the 53a6 topology of POPC from lipidbook, which
includes a double bond. The bond and angle types should be the same, but I
would expect a difference for dihedrals since in my case there are two
double bonds in a row.

Yes, to the CGenFF website. OK, I will not care too much so.

2016-12-21 3:16 GMT+01:00 Justin Lemkul :

>
>
> On 12/19/16 9:43 AM, Sim gmx wrote:
>
>> Again, thanks a lot for taking the time to reply me.
>>
>> So you think I should submit this model compound to ATB as a "starting
>> block" for my molecule ?
>> Actually my whole molecule looks like this:
>>
>> (ring system)-(C=O)-CH=CH-CH=CH-CH2-CH2-CH2-CH2-CH3
>>
>> So there is this annoying second double bond that (I guess) I am obliged
>> to
>> include into the model I would submit to ATB. Thus I have the feeling that
>> the shortest molecule that I could use as a model compound would be:
>>
>> (ring system)-(C=O)-CH=CH-CH=CH-CH3
>>
>> which is my whole molecule minus butane. So, couldn't I use the
>> ATB-topology of my whole molecule (that I already have) and change these
>> last methyl groups that should not carry any charge ?
>>
>> I would do two things:
>
> (ring system)-(C=O)-CH3
>
> and then
>
> (ring system)-(C=O)-CH=CH-CH=CH-CH2-CH3
>
> This will tell you how you might have to reapportion some of the charges,
> as the neighboring CH2 might correctly be assigned some small charge and
> having it as a terminal atom may not be wise.  The terminal CH3 in the
> model is the (n-3) carbon; each of these last three should have zero
> charge, so you can adjust the charges as needed if anything is assigned
> from the model.
>
> Nice to read your considerations about Berger and gromos FF, I easily hung
>> up on those things... (if/when you have some time, you can get a
>> confirmation here
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
>> /2016-December/109831.html
>> )
>>
>>
>> OK, it sounds great indeed, I should definitely have a look at this FF. Is
>> it possible to quickly get started with CHARMM ? Possible to launch the
>> first simulations in one week or so ? Also, I get a warning message when
>> trying to connect to CGenFF ("unsafe connexion"), should I ignore this ?
>>
>>
> To the CGenFF website?  There should be no security issues; maybe the
> certificate is out of date.
>
> -Justin
>
>
> Thank you, have a nice day !
>>
>> 2016-12-19 14:13 GMT+01:00 Justin Lemkul :
>>
>>
>>>
>>> On 12/19/16 7:50 AM, Sim gmx wrote:
>>>
>>> Thank you for your answer.

 "Unfortunately", this molecule has a peculiar structure with a 5-atoms
 cycle (including a nitrogen atom) directly bound to a C=O itself bound
 to
 a
 CH involved in a double bound. I guess that this nearness between the
 groups should lead to some "hardly predictable" charge distribution
 within
 the molecule. Hence, if I submit for instance only the 5-atoms cyclic
 part
 to ATB and take the C=O parameters from an existing topology, I guess I
 will have a hard time to merge the two parts, am I wrong ?

 If I don't get you wrong, my 'instinctive behavior' shares some
 similarities with what you suggest (replacing, wherever it is possible,
 ATB
 parameters by 'known parameters'). But if I don't  submit the whole
 molecule to ATB, then I don't know how to get "reliable" atomic charges
 ?


 This is common to all additive force fields.  You need a suitable model
>>> compound, one that includes linker portions that can be merged with
>>> neighboring functional groups by combining charges and applying/modifying
>>> known dihedrals. What I would do is try to parametrize:
>>>
>>> (ring system)-C=O-CH=CH-CH3
>>>
>>> and whatever might be a suitable flanking group for the ring (e.g. methyl
>>> or ethyl, etc) if it is in the middle of the acyl chain.  There may be
>>> partial charges on those neighboring methyl/methylene groups.  That would
>>> be normal. But putting partial charges on UA carbon atoms multiple bonds
>>> away is not intuitive, given the philosophy of the force field.  I would
>>> assume positive-positive repulsion would perturb the bilayer, unless the
>>> LJ
>>> mask the issue.
>>>
>>> You underline another important thing to consider: the choice of the
>>> right
>>>
 forcefield. Until now I've been working with berger lipids as forcefield
 for my bilayers (initially following one of your tutorials, by the way
 thanks a lot for this very helpful work !) in combination with small
 gromos53a6 molecules. Here, since my molecule includes a large acyl
 chain,
 it could be non ideal to use gromos53a6 parameters while the lipids with
 which it should 

Re: [gmx-users] Energy minimization steps

[Syed Azeem]

Thank you Alex and Mark for your replies. :-)

Azeem

> Hi,
>
> How many steps does it take you to walk down a mountain to a certain
> village? :-) Depends where you are on the mountain, and what's in the way.
> But if all you need is to be somewhere near the valley floor to start
> equilibration, anything goes!
>
> Mark
>
> On Wed, 21 Dec 2016 17:11 Alex  wrote:
>
>> This isn't a Gromacs-specific parameter, or, for that matter, anything
>> that straightforwardly depends on the nature of the system
>> (solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial
>> cases. The max number of minimization steps is something that limits an
>> energy minimization attempt, given the minimization algorithm,
>> tolerance, the energy step, and, of course, how well-behaved you expect
>> your system to be. It is a reasonable trial and error guess aimed at
>> computational efficiency, e.g. not exceeding a certain amount of
>> computational burden for really bad structures. Alternatively, limiting
>> the number of minimization steps can help not produce some kind of a
>> freaky structure when you have several local minima nearby.
>>
>>
>> Alex
>>
>>
>> On 12/20/2016 10:51 PM, Syed Azeem wrote:
>> > Hi all,
>> >
>> > What is the basis of inputting the maximum number of energy
>> > minimization steps in GROMACS?
>> > Does maximum number of energy minimization steps depend on the number
>> > of residues?
>> >
>> > I came across many articles wherein the authors have described the
>> > number of energy minimization steps within which they have minimized
>> > their protein.
>> >
>> > I have a protein of 596 residues to be simulated.
>> >
>> > Thanks in advance
>> >
>> > Azeem
>>
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Re: [gmx-users] Protein-Peptide Simulation help

[Syed Azeem]

Thanks for your reply.

Azeem

On 12/21/16, gromacs.org_gmx-users-requ...@maillist.sys.kth.se
 wrote:
> Send gromacs.org_gmx-users mailing list submissions to
>   gromacs.org_gmx-users@maillist.sys.kth.se
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> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. Re: Charge on drug (Justin Lemkul)
>2. Re: Protein-Peptide Simulation help (Justin Lemkul)
>3. Re: martini lipids self-assembly pressure coupling (Justin Lemkul)
>4. Re: Should I restrain omega dihedrals or just phi/psi?
>   (Justin Lemkul)
>5. Re: TIP3 water problem (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Tue, 20 Dec 2016 21:18:20 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Charge on drug
> Message-ID: <424fbea6-7255-9608-9e80-892995d8b...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/19/16 1:23 PM, tasneem kausar wrote:
>> Thank you for reply
>> What type of refinements are needed in topolgy file.
>> I have created the topology file from pdb file. Mol2 was converted into
>> pdb
>> and sdf of pubchem was converted into mol2.
>> So sdf to mol2 to pdb.
>> And please suggest me the right choice of server for itp file generation.
>>
>
> Check the bond length parameters and make sure your coordinate file matches
> the
> order of the atoms in the topology.  Don't ignore warnings from grompp.
>
> -Justin
>
>> Thanks in advance
>>
>> On 19 Dec 2016 18:31, "Justin Lemkul"  wrote:
>>>
>>>
>>>
>>> On 12/19/16 5:31 AM, tasneem kausar wrote:

 Thanks for reply

 I have visualized solvate.gro and em.gro. Some bonds that are not
 present
 in box.gro is seen in em.gro.
 I am giving you the link of the file to visualize.
 https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE
 https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM
>>>
>>>
>>> You have an amide group that distorts, bringing the carbonyl C closer to
>> the amide proton, which VMD then fictitiously assigns as a C-H bond.  The
>> C-N bond is much too short.  This suggests your topology is of
>> insufficient
>> quality for doing simulations and requires refinement.  There is, of
>> course, no actual bond there, as Mark has pointed out.  Visualization
>> software tries to guess where bonds should be based on interatomic
>> distances.  The topology is definitive. What you see on your screen is
>> not.
>>>
>>>
 I addition to that I have done energy minimization multiple times with
 steepest decent and conjugate gradient method. Potential energy value
 is
 negative in every minimization. When I am trying position restrain core
 dump with multiple lincs warning occurs.
>>>
>>>
>>> Your topology needs work.  It will not be stable for any simulation.
>>>
>>> -Justin
>>>
>>>
 Please tell me how this problem would be resolved

 On Mon, Dec 19, 2016 at 1:52 PM, Mark Abraham
 
 wrote:

> Hi,
>
> Your energy minimization literally cannot create bonds because those
> are
> already defined by your topology. See
>
>> http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#
> Topology_bonds_vs_Rendered_bonds
> for what's probably going on.
>
> Mark
>
> On Mon, 19 Dec 2016 19:05 tasneem kausar 
> wrote:
>
>> Dear All
>>
>>
>> I am using Acpype server to generate topology file of drug molecule
>> to
>> perform protein drug MD simulation. Acpype have generated the itp
>> file
>
> and
>>
>> other necessary for MD simulations. I am doing MD on gromacs 5.1.4
>
> software
>>
>> using amber99sb force field. When I have done energy minimization
>> some
>> unwanted bonds are formed in drug molecule. So the position restraint
>> is
>> not able to execute. The problem is due to the unusual bond in drug
>> atom.
>> When I used the itp file of PRODRG server position restraint goes
>> successfully. I have used the gromos54a7 ff. But there is problem
>> with
>
> the
>>
>> charge present on the atom that comes from PRODRG.
>>
>> Please tell me how charge on the atom can be corrected in itp file of
>> PRODRG.  How the problem in energy minimization with the Acpype itp
>> will
>
> be