Re: [gmx-users] pulling of a molecule through protein-membrane system

[Alex Mathew]

Dear Justin,
Well, Charmm-gui not providing an option to make a long box in one
direction. So is it fine increasing the box and adding the water in
Charmm-gui output pdb file and proceed?
-- 
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[gmx-users] Reg. Umbrella sampling problem with direction

[가디 장데부 고라크스나트]

Hello Everyone,


I am novice in umbrella sampling. I did followed Dr. Justin's tutorial and it 
works fine for me. However, I would like to transport solute (along z-axis) 
from an ion channel (intracellular to extracellular site) so I made the system 
(Protein+solute+DPPC+Sol+ion) and came upto the Step 5 of tutorial 
successfully. Now I wanted to get the distances among frames using perl 
distance.pl but I just get the frame number. So, I seek your advice and 
suggestion on the input parameter of Pull-code.

Here is the pull-code I used for the simulation. 

; Pull code
pull = yes
pull_ngroups  = 2
pull_ncoords  = 1
pull_group1_name= Protein
pull_group2_name= DRG
pull_coord1_type  = umbrella  ; harmonic biasing force
pull_coord1_geometry  = direction
pull_coord1_groups  = 1 2
pull_coord1_dim   = N N Y
pull_coord1_vec= 0 0 1
pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k= 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0


Please guide in making correct input parameter for pull-code 

I get this output in pullx.xvg file

@title "Pull COM"
@xaxis  label "Time (ps)"
@yaxis  label "Position (nm)"
@TYPE xy
0. -2.51551
0.1000 -2.50136
0.2000 -2.49201
0.3000 -2.49526
0.4000 -2.47566
0.5000 -2.4618
0.6000 -2.47792
0.7000 -2.47152
0.8000 -2.48659
0.9000 -2.49259
1. -2.53279
1.1000 -2.53133
1.2000 -2.51926
1.3000 -2.51488
Or how can I use this output to calculate the distance among the frames and 
further use for g_wham program.




Looking forward to interact with you.
Regards,

Changdev
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Re: [gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

I have found

However, if one wants *acpype* just to emulate *amb2gmx.pl*, one needs
nothing
at all but *[http://www.python.org Python]*.

At the moment, *acpype* is only available for download via *svn*:

  * `svn checkout http://acpype.googlecode.com/svn/trunk/ acpype`

Yet, if some reason you cannot use *svn*, one still can get *acpype* with:

  * `wget http://acpype.googlecode.com/svn/trunk/acpype.py`

But be aware that one may run in extra troubles and I am not willing to
support
this way.

== To Test ==

At folder *acpype/test*, type:

  * `../acpype.py -i FFF.pdb`

It'll create a folder called *FFF.acpype*, and inside it one may find
topology
files for GROMACS and CNS/XPLOR.


On Tue, Aug 1, 2017 at 3:00 PM, Mark Abraham 
wrote:

> Hi,
>
> Have you read the acpype documentation before trying to use it?
>
> Mark
>
> On Tue, 1 Aug 2017 23:19 Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com>
> wrote:
>
> > Dear Sir
> >
> > I have just use acpype.py -i OAI.pdb
> > I am getting the error:
> > ERROR: no 'antechamber' executable!
> > ERROR: no 'antechamber' executable... aborting !
> > ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
> > ==> HINT2: is 'antechamber' in your $PATH?
> > What 'which antechamber' in your terminal says?
> > 'alias' doesn't work for ACPYPE.
> > ACPYPE FAILED: 1
> > Total time of execution: less than a second
> >
> > I am thinking that I have to install amber. But I dont want to do that.
> Is
> > there any way that I can create ligand topology for gaff.
> >
> >
> >
> > On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
> > >
> > >> Ok, you should not mix and match forcefields, ¿but in the case of
> > >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
> > >>
> > >
> > > GAFF is compatible with AMBER (by design).  My comments were warning
> that
> > > one should not use AMBER for a protein in concert with GROMOS for a
> > ligand.
> > >
> > > -Justin
> > >
> > > Best regards.
> > >> Lucio Montero.
> > >>
> > >> Enviado desde Correo para Windows 10
> > >>
> > >> De: Alan
> > >> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
> > >> Para: Gromacs
> > >> Asunto: Re: [gmx-users] ligand topology
> > >>
> > >> Please this GitHub link is totally outdated and not linked in any
> sense
> > to
> > >> the original authors.
> > >>
> > >> Get the correct ACPYPE here:
> > >>
> > >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
> > >> stable/ccpn/python/acpype acpype
> > >>
> > >> On 1 August 2017 at 15:00, Suhaib Shekfeh 
> wrote:
> > >>
> > >> Actually, GAFF forcefield and amber forcefields are compatible. gaff
> is
> > >>> simply amber ff for small molecules.
> > >>> You have to get first amber tools. The last release is amber tools 16
> > >>> Get the source code from here :
> > >>> http://ambermd.org/AmberTools16-get.html
> > >>>
> > >>> after installation you can use antechamber for creating the
> > >>> small-molecule
> > >>> parameters
> > >>>
> > >>> later, you can use a nice free program called ACEPYP, made to convert
> > >>> amber
> > >>> parameters to gromacs toplogyget the code from here:
> > >>>
> > >>> https://github.com/t-/acpype
> > >>>
> > >>> Regards
> > >>>
> > >>>
> > >>>
> > >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> > >>> za.par...@gmail.com> wrote:
> > >>>
> > >>> Dear Sir
> > 
> >  Thank you very much for your reply. Can you give me any link or
> > 
> > >>> suggestion
> > >>>
> >  that i can learn for amber force field for protein and ligand.
> > 
> >  On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul 
> > wrote:
> > 
> > 
> > >
> > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> > >
> > > Dear Sir
> > >>
> > >> I am new for protein-ligand complex. I want amber force field
> (ff03)
> > >>
> > > for
> > >>>
> >  my
> > >> protein, tip3p for water model and gaff (General Amber force
> field)
> > >>
> > > for
> > >>>
> >  ligand. I do not know how to produce gaff force field from pdb and
> > >>
> > > then
> > >>>
> >  convert for gromacs topology.
> > >>
> > >> I have tried ff03 with gromos ligand topology and tip3p water
> model
> > >>
> > >> it gives me the error:
> > >> atomtype OM not found
> > >>
> > >> and when I have tried ff03 with gromos topology and spc water
> model
> > it
> > >> gives me the error like:
> > >> atomtype HW not found.
> > >>
> > >> Can anyone help me about it?
> > >>
> > >>
> > >> You can't mix and match force fields; it's fundamentally wrong.
> You
> > >
> >  need
> > >>>
> >  to develop ligand parameters that are consistent with the parent
> > >
> >  protein
> > >>>
> >  force field.  Various tools exist for different force fields, with
> > >
> >  varying
> > 
> > > degrees of r

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Justin Lemkul]

On 8/1/17 6:07 PM, Ali Ahmed wrote:

Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.
--
Here is what I get before crashing. Too many warning then crush.



This is not diagnostic of anything useful.  You've been asked several times to 
provide the output of grompp, not mdrun.  The grompp output can be suggestive of 
issues you may not have considered.


-Justin


Step 37, time 0.037 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 0.002768, max 0.195102 (between atoms 34930 and 34931)

bonds that rotated more than 30 degrees:

  atom 1 atom 2  angle  previous, current, constraint length

 193194   51.70.1100   0.1100  0.1100

   54409  54410   32.30.1100   0.1100  0.1100

On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
wrote:


Copy the output from both of those commands, most importantly (as Mark
has asked) that from the first one gmx grompp

You need to show people exactly what you are seeing, not what you say
you are seeing.  The latter you are filtering it, and most likely not
providing all the important information.  The former allows those
trying to help to see all the information that they need to see.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On 2 August 2017 at 04:05, Ali Ahmed  wrote:

Hi,
Thank you for your help.

well I used this command

gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

and I got all the warnings. Here is my em.mdp


-


integrator = steep

emtol   = 10.0

emstep  = 0.001

nsteps  = 5

energygrps   = system

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions

nstlist   = 1

cutoff-scheme   = group

ns_type= grid

coulombtype= PME

rcoulomb = 1.0

rvdw= 1.0

pbc  = xyz

On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham 
wrote:


Hi,

No, only mdrun issues LINCS warnings. grompp issues different warnings,

and

I would like you to check whether you had any from grompp that you may

not

have considered. :-)

Mark

On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed  wrote:


Dear Mark
Yes, all the warnings are from grompp.
I have no idea where is the problem in the structure or the topology
Thank you

On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <

mark.j.abra...@gmail.com>

wrote:


Hi,

Did you get any warnings from grompp?

Mark

On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed 

wrote:



Hello GROMACS users,

I'm doing MD for nitrogen, and for better electrostatic

interactions

I

need

to use massless and charged virtual site. I did that but when I

try

to

do

energy minimization gives me LINCS warning and crush. I don't know

where

is

the error I tried a lot but could not find a solution.
Anyone has an idea where is my error

Here is the topology file (hand written)

--

[ defaults ]

1 3 yes 0.5 0.5



;


[ atomtypes ]

; name  bond_typemasscharge   ptype  sigma

epsilon


   OP   OP0.000   0.000A  0.330

0.3062

;

nitrogen

   M  M  0.000   0.000V  0.000

0.000

;

virtual site







[ moleculetype ]

; name  nrexcl

N2 2



[ atoms ]

;   nr   typeresnr residue  atom   cgnr   charge mass

  1 OP  1N2 N1  1-0.482

14.0067


  2 M 1N2 M1  1 0.964 0.000

  3 OP   1N2 N2  1-0.482

  14.0067




[ constraints ]

; the N-N is fixed

 1   3   1   0.11



[ virtual_sites2 ]

; site  ai  aj  funct   a

  2   1   3  1   0.5000  ; right in the mid





[ system ]

N2 in vacuo



[ molecules ]

N2 1500


--

Here is the structure (N2.pdb)

---

TITLE N2 with dummy masses

REMARKTHIS IS A SIMULATION BOX

MODEL1

COMPNDUNNAMED

AUTHORGENERATED BY OPEN BABEL 2.3.2

CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1

  1


ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
0.00   N

ATOM  

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Ali Ahmed]

Dear Dr. Dallas,
Thank you for your reply. Actually, I'm new to GROMACS and
I appreciate your support.
--
Here is what I get before crashing. Too many warning then crush.

Step 37, time 0.037 (ps)  LINCS WARNING

relative constraint deviation after LINCS:

rms 0.002768, max 0.195102 (between atoms 34930 and 34931)

bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

193194   51.70.1100   0.1100  0.1100

  54409  54410   32.30.1100   0.1100  0.1100

On Tue, Aug 1, 2017 at 4:49 PM, Dallas Warren 
wrote:

> Copy the output from both of those commands, most importantly (as Mark
> has asked) that from the first one gmx grompp
>
> You need to show people exactly what you are seeing, not what you say
> you are seeing.  The latter you are filtering it, and most likely not
> providing all the important information.  The former allows those
> trying to help to see all the information that they need to see.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 2 August 2017 at 04:05, Ali Ahmed  wrote:
> > Hi,
> > Thank you for your help.
> >
> > well I used this command
> >
> > gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
> > gmx mdrun -v -deffnm em
> >
> > and I got all the warnings. Here is my em.mdp
> > 
> -
> >
> > integrator = steep
> >
> > emtol   = 10.0
> >
> > emstep  = 0.001
> >
> > nsteps  = 5
> >
> > energygrps   = system
> >
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the interactions
> >
> > nstlist   = 1
> >
> > cutoff-scheme   = group
> >
> > ns_type= grid
> >
> > coulombtype= PME
> >
> > rcoulomb = 1.0
> >
> > rvdw= 1.0
> >
> > pbc  = xyz
> >
> > On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham 
> > wrote:
> >
> >> Hi,
> >>
> >> No, only mdrun issues LINCS warnings. grompp issues different warnings,
> and
> >> I would like you to check whether you had any from grompp that you may
> not
> >> have considered. :-)
> >>
> >> Mark
> >>
> >> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed  wrote:
> >>
> >> > Dear Mark
> >> > Yes, all the warnings are from grompp.
> >> > I have no idea where is the problem in the structure or the topology
> >> > Thank you
> >> >
> >> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <
> mark.j.abra...@gmail.com>
> >> > wrote:
> >> >
> >> > > Hi,
> >> > >
> >> > > Did you get any warnings from grompp?
> >> > >
> >> > > Mark
> >> > >
> >> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed 
> wrote:
> >> > >
> >> > > > Hello GROMACS users,
> >> > > >
> >> > > > I'm doing MD for nitrogen, and for better electrostatic
> interactions
> >> I
> >> > > need
> >> > > > to use massless and charged virtual site. I did that but when I
> try
> >> to
> >> > do
> >> > > > energy minimization gives me LINCS warning and crush. I don't know
> >> > where
> >> > > is
> >> > > > the error I tried a lot but could not find a solution.
> >> > > > Anyone has an idea where is my error
> >> > > >
> >> > > > Here is the topology file (hand written)
> >> > > >
> >> > > > --
> >> > > >
> >> > > > [ defaults ]
> >> > > >
> >> > > > 1 3 yes 0.5 0.5
> >> > > >
> >> > > > 
> >> > > ;
> >> > > >
> >> > > > [ atomtypes ]
> >> > > >
> >> > > > ; name  bond_typemasscharge   ptype  sigma
> >> epsilon
> >> > > >
> >> > > >   OP   OP0.000   0.000A  0.330
> >> 0.3062
> >> > ;
> >> > > > nitrogen
> >> > > >
> >> > > >   M  M  0.000   0.000V  0.000
> >> > 0.000
> >> > > ;
> >> > > > virtual site
> >> > > >
> >> > > >
> >> > > > 
> >> > > 
> >> > > >
> >> > > > [ moleculetype ]
> >> > > >
> >> > > > ; name  nrexcl
> >> > > >
> >> > > > N2 2
> >> > > >
> >> > > >
> >> > > >
> >> > > > [ atoms ]
> >> > > >
> >> > > > ;   nr   typeresnr residue  atom   cgnr   charge mass
> >> > > >
> >> > > >  1 OP  1N2 N1  1-0.482
> 14.0067
> >> > > >
> >> > > >  2 M 1N2 M1  1 0.964 0.000
> >> > > >
> >> > > >  3 OP   1N2 N2  1-0.482
>  14.0067
> >> > > >
> >> > > >
> >> > > >
> >> > > > [ constrai

Re: [gmx-users] ligand topology

[Mark Abraham]

Hi,

Have you read the acpype documentation before trying to use it?

Mark

On Tue, 1 Aug 2017 23:19 Mohammad Zahidul Hossain Khan 
wrote:

> Dear Sir
>
> I have just use acpype.py -i OAI.pdb
> I am getting the error:
> ERROR: no 'antechamber' executable!
> ERROR: no 'antechamber' executable... aborting !
> ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
> ==> HINT2: is 'antechamber' in your $PATH?
> What 'which antechamber' in your terminal says?
> 'alias' doesn't work for ACPYPE.
> ACPYPE FAILED: 1
> Total time of execution: less than a second
>
> I am thinking that I have to install amber. But I dont want to do that. Is
> there any way that I can create ligand topology for gaff.
>
>
>
> On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
> >
> >> Ok, you should not mix and match forcefields, ¿but in the case of
> >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
> >>
> >
> > GAFF is compatible with AMBER (by design).  My comments were warning that
> > one should not use AMBER for a protein in concert with GROMOS for a
> ligand.
> >
> > -Justin
> >
> > Best regards.
> >> Lucio Montero.
> >>
> >> Enviado desde Correo para Windows 10
> >>
> >> De: Alan
> >> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
> >> Para: Gromacs
> >> Asunto: Re: [gmx-users] ligand topology
> >>
> >> Please this GitHub link is totally outdated and not linked in any sense
> to
> >> the original authors.
> >>
> >> Get the correct ACPYPE here:
> >>
> >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
> >> stable/ccpn/python/acpype acpype
> >>
> >> On 1 August 2017 at 15:00, Suhaib Shekfeh  wrote:
> >>
> >> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> >>> simply amber ff for small molecules.
> >>> You have to get first amber tools. The last release is amber tools 16
> >>> Get the source code from here :
> >>> http://ambermd.org/AmberTools16-get.html
> >>>
> >>> after installation you can use antechamber for creating the
> >>> small-molecule
> >>> parameters
> >>>
> >>> later, you can use a nice free program called ACEPYP, made to convert
> >>> amber
> >>> parameters to gromacs toplogyget the code from here:
> >>>
> >>> https://github.com/t-/acpype
> >>>
> >>> Regards
> >>>
> >>>
> >>>
> >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> >>> za.par...@gmail.com> wrote:
> >>>
> >>> Dear Sir
> 
>  Thank you very much for your reply. Can you give me any link or
> 
> >>> suggestion
> >>>
>  that i can learn for amber force field for protein and ligand.
> 
>  On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul 
> wrote:
> 
> 
> >
> > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> >
> > Dear Sir
> >>
> >> I am new for protein-ligand complex. I want amber force field (ff03)
> >>
> > for
> >>>
>  my
> >> protein, tip3p for water model and gaff (General Amber force field)
> >>
> > for
> >>>
>  ligand. I do not know how to produce gaff force field from pdb and
> >>
> > then
> >>>
>  convert for gromacs topology.
> >>
> >> I have tried ff03 with gromos ligand topology and tip3p water model
> >>
> >> it gives me the error:
> >> atomtype OM not found
> >>
> >> and when I have tried ff03 with gromos topology and spc water model
> it
> >> gives me the error like:
> >> atomtype HW not found.
> >>
> >> Can anyone help me about it?
> >>
> >>
> >> You can't mix and match force fields; it's fundamentally wrong.  You
> >
>  need
> >>>
>  to develop ligand parameters that are consistent with the parent
> >
>  protein
> >>>
>  force field.  Various tools exist for different force fields, with
> >
>  varying
> 
> > degrees of reliability.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> >
> 
> >

Re: [gmx-users] ligand topology

[Alan]

http://webapps.ccpn.ac.uk/acpype/

On 1 August 2017 at 22:18, Mohammad Zahidul Hossain Khan <
za.par...@gmail.com> wrote:

> Dear Sir
>
> I have just use acpype.py -i OAI.pdb
> I am getting the error:
> ERROR: no 'antechamber' executable!
> ERROR: no 'antechamber' executable... aborting !
> ==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
> ==> HINT2: is 'antechamber' in your $PATH?
> What 'which antechamber' in your terminal says?
> 'alias' doesn't work for ACPYPE.
> ACPYPE FAILED: 1
> Total time of execution: less than a second
>
> I am thinking that I have to install amber. But I dont want to do that. Is
> there any way that I can create ligand topology for gaff.
>
>
>
> On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
> >
> >> Ok, you should not mix and match forcefields, ¿but in the case of
> >> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
> >>
> >
> > GAFF is compatible with AMBER (by design).  My comments were warning that
> > one should not use AMBER for a protein in concert with GROMOS for a
> ligand.
> >
> > -Justin
> >
> > Best regards.
> >> Lucio Montero.
> >>
> >> Enviado desde Correo para Windows 10
> >>
> >> De: Alan
> >> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
> >> Para: Gromacs
> >> Asunto: Re: [gmx-users] ligand topology
> >>
> >> Please this GitHub link is totally outdated and not linked in any sense
> to
> >> the original authors.
> >>
> >> Get the correct ACPYPE here:
> >>
> >> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
> >> stable/ccpn/python/acpype acpype
> >>
> >> On 1 August 2017 at 15:00, Suhaib Shekfeh  wrote:
> >>
> >> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> >>> simply amber ff for small molecules.
> >>> You have to get first amber tools. The last release is amber tools 16
> >>> Get the source code from here :
> >>> http://ambermd.org/AmberTools16-get.html
> >>>
> >>> after installation you can use antechamber for creating the
> >>> small-molecule
> >>> parameters
> >>>
> >>> later, you can use a nice free program called ACEPYP, made to convert
> >>> amber
> >>> parameters to gromacs toplogyget the code from here:
> >>>
> >>> https://github.com/t-/acpype
> >>>
> >>> Regards
> >>>
> >>>
> >>>
> >>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> >>> za.par...@gmail.com> wrote:
> >>>
> >>> Dear Sir
> 
>  Thank you very much for your reply. Can you give me any link or
> 
> >>> suggestion
> >>>
>  that i can learn for amber force field for protein and ligand.
> 
>  On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul 
> wrote:
> 
> 
> >
> > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> >
> > Dear Sir
> >>
> >> I am new for protein-ligand complex. I want amber force field (ff03)
> >>
> > for
> >>>
>  my
> >> protein, tip3p for water model and gaff (General Amber force field)
> >>
> > for
> >>>
>  ligand. I do not know how to produce gaff force field from pdb and
> >>
> > then
> >>>
>  convert for gromacs topology.
> >>
> >> I have tried ff03 with gromos ligand topology and tip3p water model
> >>
> >> it gives me the error:
> >> atomtype OM not found
> >>
> >> and when I have tried ff03 with gromos topology and spc water model
> it
> >> gives me the error like:
> >> atomtype HW not found.
> >>
> >> Can anyone help me about it?
> >>
> >>
> >> You can't mix and match force fields; it's fundamentally wrong.  You
> >
>  need
> >>>
>  to develop ligand parameters that are consistent with the parent
> >
>  protein
> >>>
>  force field.  Various tools exist for different force fields, with
> >
>  varying
> 
> > degrees of reliability.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> >
> 
> 
>  --
> >

Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Dallas Warren]

Copy the output from both of those commands, most importantly (as Mark
has asked) that from the first one gmx grompp

You need to show people exactly what you are seeing, not what you say
you are seeing.  The latter you are filtering it, and most likely not
providing all the important information.  The former allows those
trying to help to see all the information that they need to see.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 2 August 2017 at 04:05, Ali Ahmed  wrote:
> Hi,
> Thank you for your help.
>
> well I used this command
>
> gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
> gmx mdrun -v -deffnm em
>
> and I got all the warnings. Here is my em.mdp
> -
>
> integrator = steep
>
> emtol   = 10.0
>
> emstep  = 0.001
>
> nsteps  = 5
>
> energygrps   = system
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
>
> nstlist   = 1
>
> cutoff-scheme   = group
>
> ns_type= grid
>
> coulombtype= PME
>
> rcoulomb = 1.0
>
> rvdw= 1.0
>
> pbc  = xyz
>
> On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> No, only mdrun issues LINCS warnings. grompp issues different warnings, and
>> I would like you to check whether you had any from grompp that you may not
>> have considered. :-)
>>
>> Mark
>>
>> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed  wrote:
>>
>> > Dear Mark
>> > Yes, all the warnings are from grompp.
>> > I have no idea where is the problem in the structure or the topology
>> > Thank you
>> >
>> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham 
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > Did you get any warnings from grompp?
>> > >
>> > > Mark
>> > >
>> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  wrote:
>> > >
>> > > > Hello GROMACS users,
>> > > >
>> > > > I'm doing MD for nitrogen, and for better electrostatic interactions
>> I
>> > > need
>> > > > to use massless and charged virtual site. I did that but when I try
>> to
>> > do
>> > > > energy minimization gives me LINCS warning and crush. I don't know
>> > where
>> > > is
>> > > > the error I tried a lot but could not find a solution.
>> > > > Anyone has an idea where is my error
>> > > >
>> > > > Here is the topology file (hand written)
>> > > >
>> > > > --
>> > > >
>> > > > [ defaults ]
>> > > >
>> > > > 1 3 yes 0.5 0.5
>> > > >
>> > > > 
>> > > ;
>> > > >
>> > > > [ atomtypes ]
>> > > >
>> > > > ; name  bond_typemasscharge   ptype  sigma
>> epsilon
>> > > >
>> > > >   OP   OP0.000   0.000A  0.330
>> 0.3062
>> > ;
>> > > > nitrogen
>> > > >
>> > > >   M  M  0.000   0.000V  0.000
>> > 0.000
>> > > ;
>> > > > virtual site
>> > > >
>> > > >
>> > > > 
>> > > 
>> > > >
>> > > > [ moleculetype ]
>> > > >
>> > > > ; name  nrexcl
>> > > >
>> > > > N2 2
>> > > >
>> > > >
>> > > >
>> > > > [ atoms ]
>> > > >
>> > > > ;   nr   typeresnr residue  atom   cgnr   charge mass
>> > > >
>> > > >  1 OP  1N2 N1  1-0.482  14.0067
>> > > >
>> > > >  2 M 1N2 M1  1 0.964 0.000
>> > > >
>> > > >  3 OP   1N2 N2  1-0.482 14.0067
>> > > >
>> > > >
>> > > >
>> > > > [ constraints ]
>> > > >
>> > > > ; the N-N is fixed
>> > > >
>> > > > 1   3   1   0.11
>> > > >
>> > > >
>> > > >
>> > > > [ virtual_sites2 ]
>> > > >
>> > > > ; site  ai  aj  funct   a
>> > > >
>> > > >  2   1   3  1   0.5000  ; right in the mid
>> > > >
>> > > >
>> > > >
>> > > > 
>> > > >
>> > > > [ system ]
>> > > >
>> > > > N2 in vacuo
>> > > >
>> > > >
>> > > >
>> > > > [ molecules ]
>> > > >
>> > > > N2 1500
>> > > >
>> > > > 
>> > > > --
>> > > >
>> > > > Here is the structure (N2.pdb)
>> > > >
>> > > > ---
>> > > >
>> > > > TITLE N2 with dummy masses
>> > > >
>> > > > REMARKTHIS IS A SIMULATION BOX
>> > > >
>> > > > MODEL1
>> > > >
>> > > > COMPNDUNNAMED
>> > > >
>> > > > AUTHORGENERATED BY OPEN BABEL 2.3.2
>> > > >
>> > > > CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1
>> > > >
>> > > > ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
>> > > > 0

Re: [gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

Dear Sir

I have just use acpype.py -i OAI.pdb
I am getting the error:
ERROR: no 'antechamber' executable!
ERROR: no 'antechamber' executable... aborting !
==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
==> HINT2: is 'antechamber' in your $PATH?
What 'which antechamber' in your terminal says?
'alias' doesn't work for ACPYPE.
ACPYPE FAILED: 1
Total time of execution: less than a second

I am thinking that I have to install amber. But I dont want to do that. Is
there any way that I can create ligand topology for gaff.



On Tue, Aug 1, 2017 at 11:41 AM, Justin Lemkul  wrote:

>
>
> On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:
>
>> Ok, you should not mix and match forcefields, ¿but in the case of
>> AMBER99SB for the protein and gaff for ligand? (TIP3P wáter).
>>
>
> GAFF is compatible with AMBER (by design).  My comments were warning that
> one should not use AMBER for a protein in concert with GROMOS for a ligand.
>
> -Justin
>
> Best regards.
>> Lucio Montero.
>>
>> Enviado desde Correo para Windows 10
>>
>> De: Alan
>> Enviado: martes, 1 de agosto de 2017 11:01 a. m.
>> Para: Gromacs
>> Asunto: Re: [gmx-users] ligand topology
>>
>> Please this GitHub link is totally outdated and not linked in any sense to
>> the original authors.
>>
>> Get the correct ACPYPE here:
>>
>> svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
>> stable/ccpn/python/acpype acpype
>>
>> On 1 August 2017 at 15:00, Suhaib Shekfeh  wrote:
>>
>> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
>>> simply amber ff for small molecules.
>>> You have to get first amber tools. The last release is amber tools 16
>>> Get the source code from here :
>>> http://ambermd.org/AmberTools16-get.html
>>>
>>> after installation you can use antechamber for creating the
>>> small-molecule
>>> parameters
>>>
>>> later, you can use a nice free program called ACEPYP, made to convert
>>> amber
>>> parameters to gromacs toplogyget the code from here:
>>>
>>> https://github.com/t-/acpype
>>>
>>> Regards
>>>
>>>
>>>
>>> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
>>> za.par...@gmail.com> wrote:
>>>
>>> Dear Sir

 Thank you very much for your reply. Can you give me any link or

>>> suggestion
>>>
 that i can learn for amber force field for protein and ligand.

 On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul  wrote:


>
> On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
>
> Dear Sir
>>
>> I am new for protein-ligand complex. I want amber force field (ff03)
>>
> for
>>>
 my
>> protein, tip3p for water model and gaff (General Amber force field)
>>
> for
>>>
 ligand. I do not know how to produce gaff force field from pdb and
>>
> then
>>>
 convert for gromacs topology.
>>
>> I have tried ff03 with gromos ligand topology and tip3p water model
>>
>> it gives me the error:
>> atomtype OM not found
>>
>> and when I have tried ff03 with gromos topology and spc water model it
>> gives me the error like:
>> atomtype HW not found.
>>
>> Can anyone help me about it?
>>
>>
>> You can't mix and match force fields; it's fundamentally wrong.  You
>
 need
>>>
 to develop ligand parameters that are consistent with the parent
>
 protein
>>>
 force field.  Various tools exist for different force fields, with
>
 varying

> degrees of reliability.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>


 --


 *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
 *Email: khan5...@vandals.uidaho.edu *
 * Skype: parash.khan2*
 *Cell: +12085967165*
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 Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] gromacs rerun calculate the energy

[Mark Abraham]

Hi,

You can't get an estimate including the long-range interaction by using a
short-ranged method. If the long range matters, it'll be wrong and if it
doesn't, you won't know that.

Mark

On Tue, 1 Aug 2017 22:43 Varvdekar Bhagyesh Rajendra <
bhagyesh.varvde...@research.iiit.ac.in> wrote:

> Dear Justin,
>
> To get an estimate of the long range interactions in LIE calculations for
> protein-ligand binding energy calculations, is it reasonable to change the
> coulomb type to reaction-field zero instead of changing the rcoulomb from
> 1.0 nanometre to half of the water box, and the coulombtype from PME to
> cut-off ? If yes, what should be the rcoulomb with coulombtype =
> reaction-field zero ?
>
> Also, instead of changing rcoulomb from 1.0 nanometre to half of the water
> box, does changing it to lets say the box length have better accuracy?
>
> Thank you,
>
> Bhagyesh
>
> - Original Message -
> From: "Justin Lemkul" 
> To: gmx-us...@gromacs.org
> Sent: Tuesday, August 1, 2017 4:20:54 AM
> Subject: Re: [gmx-users] gromacs rerun calculate the energy
>
> On 7/31/17 8:03 AM, 王珍 wrote:
> > Hi all,
> >I used Gromacs run the biological system,  which contains water,
> ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the
> coulombtype was PME and the cutoff was 10 angstrom,  then I want to use the
> commond rerun to calculate the interaction of resid 1 and resid 2, I add
> the energygrps in my mdp, and the coulombtype was PME, the .edr file can be
> obtained. Then I use g_energy to calculate the coulomb interaction. I have
> three question.
> > first, when the rcoulomb=10 angstrom, and coulombtype=PME, within 10
> angstrom, is PME algorithm using ?
> >
>
> Yes, because there are both real-space (within rcoulomb) and Fourier space
> (long-range) terms.
>
> >
> >
> > second, The PME algorithm dived into long range interaction and short
> range interaction, whereas we only calculate the short range of the coulomb
> energy using Gromacs, can we obtain the long range of the coulomb energy?
> >
>
> Perhaps by clever use of convert-tpr to zero out charges of certain groups
> (there is a post in the archive from some time ago about this) but I am
> skeptical about the value of such a number.
>
> >
> >
> > Third, when I use rerun to calculate the coulomb energy, the rcoulomb
> from 1.0 nanometre change to half of the water box I built, and the
> coulombtype from PME to cut-off, is it reasonable to calculate the coulomb
> energy?
> >
>
> This is probably the more straightforward way to determine a reasonable
> estimate
> of the longer-range energy contributions.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] Doubt about hessian matrix in Normal mode analysis

[Varvdekar Bhagyesh Rajendra]

Dear all,

I used the following command to print ascii format of the hessian matrix to a 
file from the default mtx format of gromacs obtained after normal mode analysis.

gmxdump_d -mtx nm.mtx > hessian_matrix.dat

I would like to confirm the way the hessian matrix is written in this new ascii 
file. Is the following way correct where the x, y, z coordinates of the first 
atom are considered, then second atom and so on and so forth in each row and 
column and the matrix elements are the second order derivatives of potential 
energy with respect to its corresponding row and column coordinates ?

Here x_i = x coordinate of the i_th atom, y_i = y coordinate of the i_th atom, 
z_i = z coordinate of the i_th atom.
And the matrix elements M are the second order of U (Potential energy) with 
respect to its corresponding row and column coordinate i.e. M = d^2 U / dx_i d_i

   | x1 | y1 | z1 | x2 | y2 | z2 | ... | x_n | y_n | z_n |
-|
x1 | M  |  M | M  |  M | M  | M  | ...
---
y1 | M  |  M | M  |  M | M  | M  | ...
--
z1 | M  |  M | M  |  M | M  | M  | ...
--
x2 | M  |  M | M  |  M | M  | M  | ...
---
y2 | M  |  M | M  |  M | M  | M  | ...
--
z2 | M  |  M | M  |  M | M  | M  | ...
--
.
.
.
x_N
y_N
z_N 
--


I got some hint from the following past thread but I would like to confirm the 
same.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-June/098468.html

Thank you,

Bhagyesh
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Re: [gmx-users] gromacs rerun calculate the energy

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

To get an estimate of the long range interactions in LIE calculations for 
protein-ligand binding energy calculations, is it reasonable to change the 
coulomb type to reaction-field zero instead of changing the rcoulomb from 1.0 
nanometre to half of the water box, and the coulombtype from PME to cut-off ? 
If yes, what should be the rcoulomb with coulombtype = reaction-field zero ?

Also, instead of changing rcoulomb from 1.0 nanometre to half of the water box, 
does changing it to lets say the box length have better accuracy?

Thank you,

Bhagyesh

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Tuesday, August 1, 2017 4:20:54 AM
Subject: Re: [gmx-users] gromacs rerun calculate the energy

On 7/31/17 8:03 AM, 王珍 wrote:
> Hi all,
>I used Gromacs run the biological system,  which contains water, 
> ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the 
> coulombtype was PME and the cutoff was 10 angstrom,  then I want to use the 
> commond rerun to calculate the interaction of resid 1 and resid 2, I add the 
> energygrps in my mdp, and the coulombtype was PME, the .edr file can be 
> obtained. Then I use g_energy to calculate the coulomb interaction. I have 
> three question.
> first, when the rcoulomb=10 angstrom, and coulombtype=PME, within 10 
> angstrom, is PME algorithm using ?
> 

Yes, because there are both real-space (within rcoulomb) and Fourier space 
(long-range) terms.

> 
> 
> second, The PME algorithm dived into long range interaction and short range 
> interaction, whereas we only calculate the short range of the coulomb energy 
> using Gromacs, can we obtain the long range of the coulomb energy?
> 

Perhaps by clever use of convert-tpr to zero out charges of certain groups 
(there is a post in the archive from some time ago about this) but I am 
skeptical about the value of such a number.

> 
> 
> Third, when I use rerun to calculate the coulomb energy, the rcoulomb from 
> 1.0 nanometre change to half of the water box I built, and the coulombtype 
> from PME to cut-off, is it reasonable to calculate the coulomb energy?
> 

This is probably the more straightforward way to determine a reasonable 
estimate 
of the longer-range energy contributions.

-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] Doubt about hessian matrix in Normal mode analysis

[Varvdekar Bhagyesh Rajendra]

Dear all,

I used the following command to print ascii format of the hessian matrix to a 
file from the default mtx format of gromacs obtained after normal mode analysis.

gmxdump_d -mtx nm.mtx > hessian_matrix.dat

I would like to confirm the way the hessian matrix is written in this new ascii 
file. Is the following way correct where the x, y, z coordinates of the first 
atom are considered, then second atom and so on and so forth in each row and 
column and the matrix elements are the second order derivatives of potential 
energy with respect to its corresponding row and column coordinates ?

Here x_i = x coordinate of the i_th atom, y_i = y coordinate of the i_th atom, 
z_i = z coordinate of the i_th atom.
And the matrix elements M are the second order of U (Potential energy) with 
respect to its corresponding row and column coordinate i.e. M = d^2 U / dx_i d_i

   | x1 | y1 | z1 | x2 | y2 | z2 | ... | x_n | y_n | z_n |
-|
x1 | M  |  M | M  |  M | M  | M  | ...
---
y1 | M  |  M | M  |  M | M  | M  | ...
--
z1 | M  |  M | M  |  M | M  | M  | ...
--
x2 | M  |  M | M  |  M | M  | M  | ...
---
y2 | M  |  M | M  |  M | M  | M  | ...
--
z2 | M  |  M | M  |  M | M  | M  | ...
--
.
.
.
x_N
y_N
z_N 
--


Thank you,

Bhagyesh
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[gmx-users] Umbrella Sampling with Direction-Periodic

[Daniel Kozuch]

Hello,

I am using a pull code with geometry=direction-periodic and attempting to
use gmx wham to construct the free energy. The pulling code is doing what I
would like it to, but as might be expected from direction-periodic, when
the pull distance is more than half the box length the distance is written
as negative.

Is there some way to have the pull files written with positive (greater
than half the box length) distance so that gmx wham will work properly? For
example, if the box is 10 nm long, I would like the pull distance to be
written as 7 nm, not -3 nm.

I have tried editing the pullx.xvg files, but as the .tpr files must still
include the original shortest periodic distance, this does not correct the
issue.

Thanks,
Dan
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[gmx-users] Doubt about hessian matrix in Normal mode analysis

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

I used the following command to print ascii format of the hessian matrix to a 
file from the default mtx format of gromacs obtained after normal mode analysis.

gmxdump_d -mtx nm.mtx > hessian_matrix.dat

I would like to confirm the way the hessian matrix is written in this new ascii 
file. Is the following way correct where the x, y, z coordinates of the first 
atom are considered, then second atom and so on and so forth in each row and 
column and the matrix elements are the second order derivatives of potential 
energy with respect to its corresponding row and column coordinates ?

Here x_i = x coordinate of the i_th atom, y_i = y coordinate of the i_th atom, 
z_i = z coordinate of the i_th atom.
And the matrix elements M are the second order of U (Potential energy) with 
respect to its corresponding row and column coordinate i.e. M = d^2 U / dx_i d_i

   | x1 | y1 | z1 | x2 | y2 | z2 | ... | x_n | y_n | z_n |
-|
x1 | M  |  M | M  |  M | M  | M  | ...
---
y1 | M  |  M | M  |  M | M  | M  | ...
--
z1 | M  |  M | M  |  M | M  | M  | ...
--
x2 | M  |  M | M  |  M | M  | M  | ...
---
y2 | M  |  M | M  |  M | M  | M  | ...
--
z2 | M  |  M | M  |  M | M  | M  | ...
--
.
.
.
x_N
y_N
z_N 
--


Thank you,

Bhagyesh
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Re: [gmx-users] pulling of a molecule through protein-membrane system

[Justin Lemkul]

On 8/1/17 10:01 AM, Alex Mathew wrote:

Dear all gromacs users,

I would like to build a protein-membrane system to perform umbrella
simulation; I need to calculate the molecule transportation by pulling it
from top to bottom. In the tutorial, it says  "Some force fields include
everything you need. For instance, it is unwise to try to literally follow
this approach for a force field like CHARMM36, as it needs no modification.
In that case, you are much better off building the system with CHARMM-GUI

.

I want to use Charmm36 force field, but I did not see any option to make a
box for US (as mentioned in US tutorial). Any suggestion how should I
proceed?



Specify large enough box dimensions in whatever direction you want (probably z) 
when building the box.  There's no specific "build a system for umbrella 
sampling" because the only consideration unique to this case is the box size.


-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] Creating Custom .rtp files

[Justin Lemkul]

On 8/1/17 10:32 AM, Momin Ahmad wrote:
please finde the files attached to this email: log-files for the 5.1.2 version 
and the 2016.3 version, also again the .rtp file and the .pdb file




The screen output seems garbled to me, with the fatal error coming before the 
force field selection, and multiple locations being used.  I can't figure out 
what's going on.  Your .rtp needs to be in the force field directory that you 
choose, either locally (within the working directory) or system-wide (wherever 
that is installed).  Note also that "CH4" and "CH41" are different, because one 
error indicates that pdb2gmx finds CH4 when your .rtp is clearly CH41.


-Justin



Am 01.08.2017 um 00:48 schrieb Justin Lemkul:



On 7/31/17 7:47 AM, Momin Ahmad wrote:

Hello,

the .rtp file is located in the same directory as the force-field. When i 
type gmx gmx2pdb . then the log shows that the right path is considered 
and loads the needed .rtp fiels that already exist in the forc-field file. 
But my custom one is ignored.




Please post the full screen output of pdb2gmx, including the force field 
selection.  If your .rtp file is not being read, it is likely misformatted, in 
which case you should either write your new residue entries in an existing 
file or upload it to a file-sharing service so we can provide feedback.


-Justin


Greets
Momin Ahmad

Am 25.07.2017 um 16:34 schrieb RAHUL SURESH:

On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad  wrote:


Hi,

I created a custom .pdb file and the associated .rtp file for the
force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the
5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3
version is a local installation in my /home/user folder. The log shows
the correct paths but does not consider my custom .rtp file.

I would recommend to check whether the rtp file location and source where
gmx  you have installed match. Apart from that I do not think any error
with version of Gromacs.


Am i doing
something wrong with the newer version? I added two simple files of my
problem. Thanks in advance.

Cheers
Momin Ahmad
Karlsruher Institut of Technology
Germany
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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] ligand topology

[Justin Lemkul]

On 8/1/17 2:23 PM, Lucio Ricardo Montero Valenzuela wrote:

Ok, you should not mix and match forcefields, ¿but in the case of AMBER99SB for 
the protein and gaff for ligand? (TIP3P wáter).


GAFF is compatible with AMBER (by design).  My comments were warning that one 
should not use AMBER for a protein in concert with GROMOS for a ligand.


-Justin


Best regards.
Lucio Montero.

Enviado desde Correo para Windows 10

De: Alan
Enviado: martes, 1 de agosto de 2017 11:01 a. m.
Para: Gromacs
Asunto: Re: [gmx-users] ligand topology

Please this GitHub link is totally outdated and not linked in any sense to
the original authors.

Get the correct ACPYPE here:

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

On 1 August 2017 at 15:00, Suhaib Shekfeh  wrote:


Actually, GAFF forcefield and amber forcefields are compatible. gaff is
simply amber ff for small molecules.
You have to get first amber tools. The last release is amber tools 16
Get the source code from here :
http://ambermd.org/AmberTools16-get.html

after installation you can use antechamber for creating the small-molecule
parameters

later, you can use a nice free program called ACEPYP, made to convert amber
parameters to gromacs toplogyget the code from here:

https://github.com/t-/acpype

Regards



On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
za.par...@gmail.com> wrote:


Dear Sir

Thank you very much for your reply. Can you give me any link or

suggestion

that i can learn for amber force field for protein and ligand.

On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul  wrote:




On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:


Dear Sir

I am new for protein-ligand complex. I want amber force field (ff03)

for

my
protein, tip3p for water model and gaff (General Amber force field)

for

ligand. I do not know how to produce gaff force field from pdb and

then

convert for gromacs topology.

I have tried ff03 with gromos ligand topology and tip3p water model

it gives me the error:
atomtype OM not found

and when I have tried ff03 with gromos topology and spc water model it
gives me the error like:
atomtype HW not found.

Can anyone help me about it?



You can't mix and match force fields; it's fundamentally wrong.  You

need

to develop ligand parameters that are consistent with the parent

protein

force field.  Various tools exist for different force fields, with

varying

degrees of reliability.

-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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--


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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--
Dr. rer. nat. Suhaib Shekfeh
PhD in Computational Drug Design and Medicinal Chemistry
Oleariusstr. 11, Halle (Saale), Germany
LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
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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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* For

Re: [gmx-users] ligand topology

[Lucio Ricardo Montero Valenzuela]

Ok, you should not mix and match forcefields, ¿but in the case of AMBER99SB for 
the protein and gaff for ligand? (TIP3P wáter).
Best regards.
Lucio Montero.

Enviado desde Correo para Windows 10

De: Alan
Enviado: martes, 1 de agosto de 2017 11:01 a. m.
Para: Gromacs
Asunto: Re: [gmx-users] ligand topology

Please this GitHub link is totally outdated and not linked in any sense to
the original authors.

Get the correct ACPYPE here:

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

On 1 August 2017 at 15:00, Suhaib Shekfeh  wrote:

> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> simply amber ff for small molecules.
> You have to get first amber tools. The last release is amber tools 16
> Get the source code from here :
> http://ambermd.org/AmberTools16-get.html
>
> after installation you can use antechamber for creating the small-molecule
> parameters
>
> later, you can use a nice free program called ACEPYP, made to convert amber
> parameters to gromacs toplogyget the code from here:
>
> https://github.com/t-/acpype
>
> Regards
>
>
>
> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com> wrote:
>
> > Dear Sir
> >
> > Thank you very much for your reply. Can you give me any link or
> suggestion
> > that i can learn for amber force field for protein and ligand.
> >
> > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> > >
> > >> Dear Sir
> > >>
> > >> I am new for protein-ligand complex. I want amber force field (ff03)
> for
> > >> my
> > >> protein, tip3p for water model and gaff (General Amber force field)
> for
> > >> ligand. I do not know how to produce gaff force field from pdb and
> then
> > >> convert for gromacs topology.
> > >>
> > >> I have tried ff03 with gromos ligand topology and tip3p water model
> > >>
> > >> it gives me the error:
> > >> atomtype OM not found
> > >>
> > >> and when I have tried ff03 with gromos topology and spc water model it
> > >> gives me the error like:
> > >> atomtype HW not found.
> > >>
> > >> Can anyone help me about it?
> > >>
> > >>
> > > You can't mix and match force fields; it's fundamentally wrong.  You
> need
> > > to develop ligand parameters that are consistent with the parent
> protein
> > > force field.  Various tools exist for different force fields, with
> > varying
> > > degrees of reliability.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> >
> >
> > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> > *Email: khan5...@vandals.uidaho.edu *
> > * Skype: parash.khan2*
> > *Cell: +12085967165*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Dr. rer. nat. Suhaib Shekfeh
> PhD in Computational Drug Design and Medicinal Chemistry
> Oleariusstr. 11, Halle (Saale), Germany
> LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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>
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>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
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Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
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Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Ali Ahmed]

Hi,
Thank you for your help.

well I used this command

gmx grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

and I got all the warnings. Here is my em.mdp
-

integrator = steep

emtol   = 10.0

emstep  = 0.001

nsteps  = 5

energygrps   = system

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions

nstlist   = 1

cutoff-scheme   = group

ns_type= grid

coulombtype= PME

rcoulomb = 1.0

rvdw= 1.0

pbc  = xyz

On Tue, Aug 1, 2017 at 11:07 AM, Mark Abraham 
wrote:

> Hi,
>
> No, only mdrun issues LINCS warnings. grompp issues different warnings, and
> I would like you to check whether you had any from grompp that you may not
> have considered. :-)
>
> Mark
>
> On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed  wrote:
>
> > Dear Mark
> > Yes, all the warnings are from grompp.
> > I have no idea where is the problem in the structure or the topology
> > Thank you
> >
> > On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Did you get any warnings from grompp?
> > >
> > > Mark
> > >
> > > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  wrote:
> > >
> > > > Hello GROMACS users,
> > > >
> > > > I'm doing MD for nitrogen, and for better electrostatic interactions
> I
> > > need
> > > > to use massless and charged virtual site. I did that but when I try
> to
> > do
> > > > energy minimization gives me LINCS warning and crush. I don't know
> > where
> > > is
> > > > the error I tried a lot but could not find a solution.
> > > > Anyone has an idea where is my error
> > > >
> > > > Here is the topology file (hand written)
> > > >
> > > > --
> > > >
> > > > [ defaults ]
> > > >
> > > > 1 3 yes 0.5 0.5
> > > >
> > > > 
> > > ;
> > > >
> > > > [ atomtypes ]
> > > >
> > > > ; name  bond_typemasscharge   ptype  sigma
> epsilon
> > > >
> > > >   OP   OP0.000   0.000A  0.330
> 0.3062
> > ;
> > > > nitrogen
> > > >
> > > >   M  M  0.000   0.000V  0.000
> > 0.000
> > > ;
> > > > virtual site
> > > >
> > > >
> > > > 
> > > 
> > > >
> > > > [ moleculetype ]
> > > >
> > > > ; name  nrexcl
> > > >
> > > > N2 2
> > > >
> > > >
> > > >
> > > > [ atoms ]
> > > >
> > > > ;   nr   typeresnr residue  atom   cgnr   charge mass
> > > >
> > > >  1 OP  1N2 N1  1-0.482  14.0067
> > > >
> > > >  2 M 1N2 M1  1 0.964 0.000
> > > >
> > > >  3 OP   1N2 N2  1-0.482 14.0067
> > > >
> > > >
> > > >
> > > > [ constraints ]
> > > >
> > > > ; the N-N is fixed
> > > >
> > > > 1   3   1   0.11
> > > >
> > > >
> > > >
> > > > [ virtual_sites2 ]
> > > >
> > > > ; site  ai  aj  funct   a
> > > >
> > > >  2   1   3  1   0.5000  ; right in the mid
> > > >
> > > >
> > > >
> > > > 
> > > >
> > > > [ system ]
> > > >
> > > > N2 in vacuo
> > > >
> > > >
> > > >
> > > > [ molecules ]
> > > >
> > > > N2 1500
> > > >
> > > > 
> > > > --
> > > >
> > > > Here is the structure (N2.pdb)
> > > >
> > > > ---
> > > >
> > > > TITLE N2 with dummy masses
> > > >
> > > > REMARKTHIS IS A SIMULATION BOX
> > > >
> > > > MODEL1
> > > >
> > > > COMPNDUNNAMED
> > > >
> > > > AUTHORGENERATED BY OPEN BABEL 2.3.2
> > > >
> > > > CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1
> > > >
> > > > ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
> > > > 0.00   N
> > > >
> > > > ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
> > > > 0.00  Xx
> > > >
> > > > ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
> > > > 0.00   N
> > > >
> > > > CONECT13
> > > >
> > > > CONECT31
> > > >
> > > > MASTER00000000303
> 0
> > > >
> > > > END0
> > > >
> > > > 
> > > > -
> > > > Thank you
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail 

Re: [gmx-users] ligand topology

[Mohammad Zahidul Hossain Khan]

Dear Sir

Thank you very much.

On Tue, Aug 1, 2017 at 7:00 AM, Suhaib Shekfeh  wrote:

> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> simply amber ff for small molecules.
> You have to get first amber tools. The last release is amber tools 16
> Get the source code from here :
> http://ambermd.org/AmberTools16-get.html
>
> after installation you can use antechamber for creating the small-molecule
> parameters
>
> later, you can use a nice free program called ACEPYP, made to convert amber
> parameters to gromacs toplogyget the code from here:
>
> https://github.com/t-/acpype
>
> Regards
>
>
>
> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com> wrote:
>
> > Dear Sir
> >
> > Thank you very much for your reply. Can you give me any link or
> suggestion
> > that i can learn for amber force field for protein and ligand.
> >
> > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> > >
> > >> Dear Sir
> > >>
> > >> I am new for protein-ligand complex. I want amber force field (ff03)
> for
> > >> my
> > >> protein, tip3p for water model and gaff (General Amber force field)
> for
> > >> ligand. I do not know how to produce gaff force field from pdb and
> then
> > >> convert for gromacs topology.
> > >>
> > >> I have tried ff03 with gromos ligand topology and tip3p water model
> > >>
> > >> it gives me the error:
> > >> atomtype OM not found
> > >>
> > >> and when I have tried ff03 with gromos topology and spc water model it
> > >> gives me the error like:
> > >> atomtype HW not found.
> > >>
> > >> Can anyone help me about it?
> > >>
> > >>
> > > You can't mix and match force fields; it's fundamentally wrong.  You
> need
> > > to develop ligand parameters that are consistent with the parent
> protein
> > > force field.  Various tools exist for different force fields, with
> > varying
> > > degrees of reliability.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> >
> >
> > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> > *Email: khan5...@vandals.uidaho.edu *
> > * Skype: parash.khan2*
> > *Cell: +12085967165*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Dr. rer. nat. Suhaib Shekfeh
> PhD in Computational Drug Design and Medicinal Chemistry
> Oleariusstr. 11, Halle (Saale), Germany
> LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Mark Abraham]

Hi,

No, only mdrun issues LINCS warnings. grompp issues different warnings, and
I would like you to check whether you had any from grompp that you may not
have considered. :-)

Mark

On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed  wrote:

> Dear Mark
> Yes, all the warnings are from grompp.
> I have no idea where is the problem in the structure or the topology
> Thank you
>
> On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Did you get any warnings from grompp?
> >
> > Mark
> >
> > On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  wrote:
> >
> > > Hello GROMACS users,
> > >
> > > I'm doing MD for nitrogen, and for better electrostatic interactions I
> > need
> > > to use massless and charged virtual site. I did that but when I try to
> do
> > > energy minimization gives me LINCS warning and crush. I don't know
> where
> > is
> > > the error I tried a lot but could not find a solution.
> > > Anyone has an idea where is my error
> > >
> > > Here is the topology file (hand written)
> > >
> > > --
> > >
> > > [ defaults ]
> > >
> > > 1 3 yes 0.5 0.5
> > >
> > > 
> > ;
> > >
> > > [ atomtypes ]
> > >
> > > ; name  bond_typemasscharge   ptype  sigma  epsilon
> > >
> > >   OP   OP0.000   0.000A  0.330  0.3062
> ;
> > > nitrogen
> > >
> > >   M  M  0.000   0.000V  0.000
> 0.000
> > ;
> > > virtual site
> > >
> > >
> > > 
> > 
> > >
> > > [ moleculetype ]
> > >
> > > ; name  nrexcl
> > >
> > > N2 2
> > >
> > >
> > >
> > > [ atoms ]
> > >
> > > ;   nr   typeresnr residue  atom   cgnr   charge mass
> > >
> > >  1 OP  1N2 N1  1-0.482  14.0067
> > >
> > >  2 M 1N2 M1  1 0.964 0.000
> > >
> > >  3 OP   1N2 N2  1-0.482 14.0067
> > >
> > >
> > >
> > > [ constraints ]
> > >
> > > ; the N-N is fixed
> > >
> > > 1   3   1   0.11
> > >
> > >
> > >
> > > [ virtual_sites2 ]
> > >
> > > ; site  ai  aj  funct   a
> > >
> > >  2   1   3  1   0.5000  ; right in the mid
> > >
> > >
> > >
> > > 
> > >
> > > [ system ]
> > >
> > > N2 in vacuo
> > >
> > >
> > >
> > > [ molecules ]
> > >
> > > N2 1500
> > >
> > > 
> > > --
> > >
> > > Here is the structure (N2.pdb)
> > >
> > > ---
> > >
> > > TITLE N2 with dummy masses
> > >
> > > REMARKTHIS IS A SIMULATION BOX
> > >
> > > MODEL1
> > >
> > > COMPNDUNNAMED
> > >
> > > AUTHORGENERATED BY OPEN BABEL 2.3.2
> > >
> > > CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1
> > >
> > > ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
> > > 0.00   N
> > >
> > > ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
> > > 0.00  Xx
> > >
> > > ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
> > > 0.00   N
> > >
> > > CONECT13
> > >
> > > CONECT31
> > >
> > > MASTER000000003030
> > >
> > > END0
> > >
> > > 
> > > -
> > > Thank you
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > 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.
> >
> --
> 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] ligand topology

[Alan]

Please this GitHub link is totally outdated and not linked in any sense to
the original authors.

Get the correct ACPYPE here:

svn checkout http://ccpn.svn.sourceforge.net/svnroot/ccpn/branches/
stable/ccpn/python/acpype acpype

On 1 August 2017 at 15:00, Suhaib Shekfeh  wrote:

> Actually, GAFF forcefield and amber forcefields are compatible. gaff is
> simply amber ff for small molecules.
> You have to get first amber tools. The last release is amber tools 16
> Get the source code from here :
> http://ambermd.org/AmberTools16-get.html
>
> after installation you can use antechamber for creating the small-molecule
> parameters
>
> later, you can use a nice free program called ACEPYP, made to convert amber
> parameters to gromacs toplogyget the code from here:
>
> https://github.com/t-/acpype
>
> Regards
>
>
>
> On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
> za.par...@gmail.com> wrote:
>
> > Dear Sir
> >
> > Thank you very much for your reply. Can you give me any link or
> suggestion
> > that i can learn for amber force field for protein and ligand.
> >
> > On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> > >
> > >> Dear Sir
> > >>
> > >> I am new for protein-ligand complex. I want amber force field (ff03)
> for
> > >> my
> > >> protein, tip3p for water model and gaff (General Amber force field)
> for
> > >> ligand. I do not know how to produce gaff force field from pdb and
> then
> > >> convert for gromacs topology.
> > >>
> > >> I have tried ff03 with gromos ligand topology and tip3p water model
> > >>
> > >> it gives me the error:
> > >> atomtype OM not found
> > >>
> > >> and when I have tried ff03 with gromos topology and spc water model it
> > >> gives me the error like:
> > >> atomtype HW not found.
> > >>
> > >> Can anyone help me about it?
> > >>
> > >>
> > > You can't mix and match force fields; it's fundamentally wrong.  You
> need
> > > to develop ligand parameters that are consistent with the parent
> protein
> > > force field.  Various tools exist for different force fields, with
> > varying
> > > degrees of reliability.
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> >
> >
> > *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> > *Email: khan5...@vandals.uidaho.edu *
> > * Skype: parash.khan2*
> > *Cell: +12085967165*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> Dr. rer. nat. Suhaib Shekfeh
> PhD in Computational Drug Design and Medicinal Chemistry
> Oleariusstr. 11, Halle (Saale), Germany
> LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Re: [gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Ali Ahmed]

Dear Mark
Yes, all the warnings are from grompp.
I have no idea where is the problem in the structure or the topology
Thank you

On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham 
wrote:

> Hi,
>
> Did you get any warnings from grompp?
>
> Mark
>
> On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed  wrote:
>
> > Hello GROMACS users,
> >
> > I'm doing MD for nitrogen, and for better electrostatic interactions I
> need
> > to use massless and charged virtual site. I did that but when I try to do
> > energy minimization gives me LINCS warning and crush. I don't know where
> is
> > the error I tried a lot but could not find a solution.
> > Anyone has an idea where is my error
> >
> > Here is the topology file (hand written)
> >
> > --
> >
> > [ defaults ]
> >
> > 1 3 yes 0.5 0.5
> >
> > 
> ;
> >
> > [ atomtypes ]
> >
> > ; name  bond_typemasscharge   ptype  sigma  epsilon
> >
> >   OP   OP0.000   0.000A  0.330  0.3062 ;
> > nitrogen
> >
> >   M  M  0.000   0.000V  0.000  0.000
> ;
> > virtual site
> >
> >
> > 
> 
> >
> > [ moleculetype ]
> >
> > ; name  nrexcl
> >
> > N2 2
> >
> >
> >
> > [ atoms ]
> >
> > ;   nr   typeresnr residue  atom   cgnr   charge mass
> >
> >  1 OP  1N2 N1  1-0.482  14.0067
> >
> >  2 M 1N2 M1  1 0.964 0.000
> >
> >  3 OP   1N2 N2  1-0.482 14.0067
> >
> >
> >
> > [ constraints ]
> >
> > ; the N-N is fixed
> >
> > 1   3   1   0.11
> >
> >
> >
> > [ virtual_sites2 ]
> >
> > ; site  ai  aj  funct   a
> >
> >  2   1   3  1   0.5000  ; right in the mid
> >
> >
> >
> > 
> >
> > [ system ]
> >
> > N2 in vacuo
> >
> >
> >
> > [ molecules ]
> >
> > N2 1500
> >
> > 
> > --
> >
> > Here is the structure (N2.pdb)
> >
> > ---
> >
> > TITLE N2 with dummy masses
> >
> > REMARKTHIS IS A SIMULATION BOX
> >
> > MODEL1
> >
> > COMPNDUNNAMED
> >
> > AUTHORGENERATED BY OPEN BABEL 2.3.2
> >
> > CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1 1
> >
> > ATOM  1  N1  N2  1   0.000   0.000   0.000  1.00
> > 0.00   N
> >
> > ATOM  2  M1  N2  1   0.55000   0.000   0.000  1.00
> > 0.00  Xx
> >
> > ATOM  3  N2  N2  1   1.100   0.000   0.000  1.00
> > 0.00   N
> >
> > CONECT13
> >
> > CONECT31
> >
> > MASTER000000003030
> >
> > END0
> >
> > 
> > -
> > Thank you
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Creating Custom .rtp files

[Momin Ahmad]

please finde the files attached to this email: log-files for the 5.1.2 
version and the 2016.3 version, also again the .rtp file and the .pdb file



Am 01.08.2017 um 00:48 schrieb Justin Lemkul:



On 7/31/17 7:47 AM, Momin Ahmad wrote:

Hello,

the .rtp file is located in the same directory as the force-field. 
When i type gmx gmx2pdb . then the log shows that the right path 
is considered and loads the needed .rtp fiels that already exist in 
the forc-field file. But my custom one is ignored.




Please post the full screen output of pdb2gmx, including the force 
field selection.  If your .rtp file is not being read, it is likely 
misformatted, in which case you should either write your new residue 
entries in an existing file or upload it to a file-sharing service so 
we can provide feedback.


-Justin


Greets
Momin Ahmad

Am 25.07.2017 um 16:34 schrieb RAHUL SURESH:
On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad  
wrote:



Hi,

I created a custom .pdb file and the associated .rtp file for the
force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for 
the

5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3
version is a local installation in my /home/user folder. The log shows
the correct paths but does not consider my custom .rtp file.
I would recommend to check whether the rtp file location and source 
where

gmx  you have installed match. Apart from that I do not think any error
with version of Gromacs.


Am i doing
something wrong with the newer version? I added two simple files of my
problem. Thanks in advance.

Cheers
Momin Ahmad
Karlsruher Institut of Technology
Germany
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Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: momin.ah...@kit.edu

  :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar   
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch 
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner  
Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff 
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk   
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers  
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf   
   and the project leaders:
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Copyright (c) 2001-2015, The GROMACS development team at
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check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
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as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
  gmx pdb2gmx -f methane.pdb

Opening force field file 
/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
 1: TIP3P TIP 3-point, recommended
 2: TIP4P TIP 4-point
 3: TIP4P-Ew  TIP 4-point optimized with Ewald
 4: TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for 
issues)
 5: SPC   simple point charge
 6: SPC/E extended simple point charge
 7: None
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b
All occupancies are one
Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp

Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
A

Re: [gmx-users] ligand topology

[Suhaib Shekfeh]

Actually, GAFF forcefield and amber forcefields are compatible. gaff is
simply amber ff for small molecules.
You have to get first amber tools. The last release is amber tools 16
Get the source code from here :
http://ambermd.org/AmberTools16-get.html

after installation you can use antechamber for creating the small-molecule
parameters

later, you can use a nice free program called ACEPYP, made to convert amber
parameters to gromacs toplogyget the code from here:

https://github.com/t-/acpype

Regards



On Tue, Aug 1, 2017 at 1:17 AM, Mohammad Zahidul Hossain Khan <
za.par...@gmail.com> wrote:

> Dear Sir
>
> Thank you very much for your reply. Can you give me any link or suggestion
> that i can learn for amber force field for protein and ligand.
>
> On Mon, Jul 31, 2017 at 3:53 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> >
> >> Dear Sir
> >>
> >> I am new for protein-ligand complex. I want amber force field (ff03) for
> >> my
> >> protein, tip3p for water model and gaff (General Amber force field) for
> >> ligand. I do not know how to produce gaff force field from pdb and then
> >> convert for gromacs topology.
> >>
> >> I have tried ff03 with gromos ligand topology and tip3p water model
> >>
> >> it gives me the error:
> >> atomtype OM not found
> >>
> >> and when I have tried ff03 with gromos topology and spc water model it
> >> gives me the error like:
> >> atomtype HW not found.
> >>
> >> Can anyone help me about it?
> >>
> >>
> > You can't mix and match force fields; it's fundamentally wrong.  You need
> > to develop ligand parameters that are consistent with the parent protein
> > force field.  Various tools exist for different force fields, with
> varying
> > degrees of reliability.
> >
> > -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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> >
>
>
>
> --
>
>
> *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
> *Email: khan5...@vandals.uidaho.edu *
> * Skype: parash.khan2*
> *Cell: +12085967165*
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-- 
Dr. rer. nat. Suhaib Shekfeh
PhD in Computational Drug Design and Medicinal Chemistry
Oleariusstr. 11, Halle (Saale), Germany
LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255
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[gmx-users] pulling of a molecule through protein-membrane system

[Alex Mathew]

Dear all gromacs users,

I would like to build a protein-membrane system to perform umbrella
simulation; I need to calculate the molecule transportation by pulling it
from top to bottom. In the tutorial, it says  "Some force fields include
everything you need. For instance, it is unwise to try to literally follow
this approach for a force field like CHARMM36, as it needs no modification.
In that case, you are much better off building the system with CHARMM-GUI

.

I want to use Charmm36 force field, but I did not see any option to make a
box for US (as mentioned in US tutorial). Any suggestion how should I
proceed?
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[gmx-users] pme algorithm

[????]

Hi all,
 
  I used Gromacs run the biological system, which contains water, 
ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the coulombtype 
was PME and the cutoff was 10 angstrom, then I want to use the commond rerun to 
calculate the interaction of resid 1 and resid 2, I add the energygrps in my 
mdp, and the coulombtype was PME, the .edr file can be obtained. Then I use 
g_energy to calculate the coulomb interaction. 

In real space, the coulomb energy using the equation  ,if using the equation  , 
are these two values different too much?




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[gmx-users] Alchemical transformation position restrains for B state and citing literature for H-RETI

[Hermann, Johannes]

Dear all,

I have two questions concerning MD free energy calculations:

1) (For some reasons) I want to restrain the backbone of my protein 
during TI. However, I do not know to correctly generate position 
restrains for the mutated B-state. If I use the position restrain file, 
which I generated for the A state, following warning shows up:


WARNING 1 [file posre.itp, line 1470]:
  Some parameters for bonded interaction involving perturbed atoms are
  specified explicitly in state A, but not B - copying A to B

Can I ignore this warning, or do you have any suggestions for me?


2) I am using replica exchange ( -replex in the mdrun) during the free 
energy thermodynamic integration MD simulation (H-RETI). Can someone 
tell me the literature I should cite when I apply this?


All the best and thank you very much in advance

Johannes

--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
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D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

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[gmx-users] Estimation of the rotations during CG simulations

[Gleb Novikov]

Dear Gromacs Users!
I am dealing with investigation of membrane receptors oligomerization in the 
MARTINI model. The case study CG model consist of big membrane with 18 embedded 
GPCRs.  I wonder to estimate rotation of each receptor monomer along its 
principal axis during simulation. Does the g_rotacf (estimation of the rotation 
diffusion) - the only way to do it or there are more trivial methods e.g to 
calculate the moment of inetria? If so, I will be grateful for some example how 
this tool can be adapted for CG models.
Thanks so much!
Gleb
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[gmx-users] PCA in dihdral space

[Gleb Novikov]

 Dear Gromacs users!

In the tutorial I found that tomake a list for dihedral angles via mk_angndxI 
need to provide tpr file as an input.  
 Here some of my questions:
1)Is itpossible to make a list from pdb file (or convert pdb to tpr),assuming 
that my trajectory has been calculated not in Gromacs ?

2) Does this method good forcalculation of PCA of Chi-1 angle of the side 
chains (e.g to clarifythe contribution of the concerned rotation of the 
side-chain)?
Thanks !

Gleb
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[gmx-users] Can not write a pdb file without atom names (concatenating 2 pdb files)

[Andrew Bostick]

Dear gromacs users,

I have 2 trajectory files as pdb format.

I want to have only one file using the following command:

gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime

I encountered with:

---

Command line:
  gmx_mpi trjcat -f 9_ms.pdb 19.pdb -o mix.pdb -settime

Reading frame   0 time0.000'c15 t= 3.0', 6250 atoms
Reading frame   0 time0.000'c15 t= 3.0', 6250 atoms
Reading frame   1 time 3.000


Enter the new start time (ps) for each file.
There are two special options, both disable sorting:

c (continue) - The start time is taken from the end
of the previous file. Use it when your continuation run
restarts with t=0.

l (last) - The time in this file will be changed the
same amount as in the previous. Use it when the time in the
new run continues from the end of the previous one,
since this takes possible overlap into account.

  File Current start (ps)  New start (ps)
-
 9_ms.pdb0.000 ps  0
   19.pdb0.000 ps  900

Summary of files and start times used:

  FileStart time   Time step
-
 9_ms.pdb0.000 ps3.000 ps
   19.pdb   900.000 ps3.000 ps


Back Off! I just backed up mix.pdb to ./#mix.pdb.4#
Reading frame   0 time0.000

Continue writing frames from 9_ms.pdb t=0 ps, frame=0

---
Program gmx trjcat, VERSION 5.1.3
Source code file:
/root/gromacs_source/gromacs-5.1.3/src/gromacs/fileio/trxio.c, line: 557

Fatal error:
Can not write a pdb file without atom names
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

---

How to resolve this issue?

Best,
Andrew
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Re: [gmx-users] Some problem about the process of calculating MM-PBSA binding free energy

[刘玉杰]

Thanks a lot！



In fact, I just can not confirm the value of pconc or nconc of the
polar.mdp, namely under what conditions  should I set “0” or “0.150”？





Yours sincerely

Yujie, liu

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