[gmx-users] UMBRELLA SAMPLING

[Subashini .K]

Hi gromacs users,


I want to perfom NVT equilibration, pull code (using pull-geometry = 
direction-periodic)


Prior to this step, energy minimization (500 steps) and NPT equilibration 
(5 steps) was done


As I am new to gromacs and simulations, can anyone tell me whether the 
following NVT code is correct?


Is this code for NVT correct?


title = Umbrella pulling simulation
define = -DPOSRES
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 5 ; 100 ps
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc_grps = Protein Non-Protein
tau_t = 0.5 0.5
ref_t = 310 310
; Pressure coupling is off
Pcoupl = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Velocity generation
gen_vel = no ;

; Pull code

..
..
.


Thanks,
Subashini.K

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[gmx-users] UMBRELLA SAMPLING

[Subashini .K]

Hi gromacs users,


I want to calculate delta G for protein ligand binding.


Had run the umbrella pulling simulation   for 100 ps (protein ligand solvated 
in water), applying restraint in the protein (using the code in gromacs 
tutorial website, Bevenlab).


But, after running the perl script  (perl distances.pl), did not obtain any 
distance on the right column (summary_distances.dat). It was blank.



(1) Had applied the position restrain of the protein during NPT equilibration.

(2) During puling simulation, again applied the restrain on the protein. Is it 
correct?


How to rectify the mistake and proceed in the right direction?



Thanks,

Subashini.K
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Re: [gmx-users] topology

[Subashini .K]

Did you try PRODRG server?




From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of RAHUL SURESH 

Sent: Thursday, March 2, 2017 9:53 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] topology

Dear Justin

Is there anything I can do to make this job easier?

On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul  wrote:

>
>
> On 3/1/17 2:19 PM, RAHUL SURESH wrote:
>
>> Dear Justin
>>
>> What is the error here?
>> I don't understand it.
>> Can you be little more precise?
>>
>>
> The long and short of it TopolGen is very crudely coded and atom order
> matters because the script makes a lot of assumptions.  Your input PDB file
> has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
> out what any of the actual functional groups are, so you get basically
> default atom types for everything.
>
> -Justin
>
>
> On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 2/28/17 3:24 AM, RAHUL SURESH wrote:
>>>
>>> This is my itp file(only a part)

 I have highlighted two errors.. there are 19 such errors.
 If I can know the reason for the error exactly it would be of a great
 help
 to me.


 TopolGen relies on atom ordering to guess what the proper parameters
>>> should be. It's pretty limited in what it can do.  A coordinate file that
>>> simply groups atoms by element is going to produce a totally garbage
>>> topology, unfortunately.
>>>
>>> -Justin
>>>
>>>
>>> [ atoms ]
 ;   nr   type  resnr residue  atom   cgnr charge   mass
 typeBchargeB  massB
  1   opls_154  1UNK  O  0 -0.580921
 15.99940
  2   opls_154  1UNK  O  0 -0.635654
 15.99940
  3   opls_516  1UNK  C  1 -0.112257
 12.01100
  4   opls_516  1UNK  C  2 -0.163224
 12.01100
  5   opls_516  1UNK  C  3  0.228741
 12.01100
  6   opls_516  1UNK  C  4 -0.304756
 12.01100
  7   opls_516  1UNK  C  5 -0.312217
 12.01100
  8   opls_145  1UNK  C  6  0.120569
 12.01100
  9   opls_145  1UNK  C  7  0.151897
 12.01100
 10   opls_145  1UNK  C  8  0.231044
 12.01100
 11   opls_516  1UNK  C  9 -0.401751
 12.01100
 12   opls_516  1UNK  C 10 -0.403094
 12.01100
 13   opls_145  1UNK  C 11 -0.150352
 12.01100
 14   opls_145  1UNK  C 12  0.193129
 12.01100
 15   opls_145  1UNK  C 13 -0.161115
 12.01100
 16   opls_516  1UNK  C 14 -0.471874
 12.01100
 17   opls_145  1UNK  C 15  0.100725
 12.01100
 18   opls_145  1UNK  C 16 -0.153943
 12.01100
 19   opls_516  1UNK  C 17 -0.330577
 12.01100
 20   opls_516  1UNK  C 18 -0.229875
 12.01100
 21   opls_135  1UNK  C 19 -0.229884
 12.01100
 22   opls_135  1UNK  C 20 -0.237230
 12.01100
 23   opls_135  1UNK  C 21 -0.404861
 12.01100
 24   opls_140  1UNK  H 21  0.135257
 1.00800
 25   opls_140  1UNK  H 21  0.154010
 1.00800
 26   opls_140  1UNK 2H 21  0.142643
 1.00800
 27   opls_140  1UNK 1H 21  0.133623
 1.00800
 28   opls_140  1UNK 2H 21  0.137323
 1.00800
 29   opls_140  1UNK 1H 21  0.167475
 1.00800
 30   opls_140  1UNK 1H 21  0.135348
 1.00800
 31   opls_140  1UNK 2H 21  0.153851
 1.00800
 32   opls_140  1UNK 3H 21  0.138487
 1.00800
 33   opls_140  1UNK 1H 21  0.137087
 1.00800
 34   opls_140  1UNK 2H 21  0.146500
 1.00800
 35   opls_140  1UNK 3H 21  0.148972
 1.00800
 36   opls_140  1UNK  H 21  0.103605
 1.00800
 37   opls_140  1UNK  H 21  0.127061
 1.00800
 38   opls_140  1UNK 1H 21  0.143100
 1.00800
 39   opls_140  1UNK 2H 21  0.137525
 1.00800
 40   opls_140  1UNK 3H 21  0.140672
 1.00800
 41   opls_140  1UNK  H 21  0.106416
 1.00800
 42   opls_140  1UNK 1H 21  

[gmx-users] HOW TO SPLIT RESIDUES

[Subashini .K]

Hi gromacs users,

How to split residue 2?

Here, there are two identical organic compounds in water.

Each compound has 29 atoms (consisting of carbon, nitrogen and hydrogen)

Gave the command splitres 2.

How to proceed after that?


0 System  :  9664 atoms
  1 Other   :58 atoms
  2 MOL :58 atoms
  3 Water   :  9606 atoms
  4 SOL :  9606 atoms
  5 non-Water   :58 atoms

 nr : group   !   'name' nr name   'splitch' nrEnter: list groups
 'a': atom&   'del' nr 'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr'splitat' nr'h': help
 'r': residue 'res' nr 'chain' char
 "name": group'case': case sensitive   'q': save and quit
 'ri': residue index

Thanks,
Subashini.K

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Re: [gmx-users] ERROR IN BASH SCRIPTING

[Subashini .K]

Hi,

Thank you for the reply.

I have fixed the error  by running the script through dos2unix.

There is an option in Notepad++.

Thank you once again.



Thanks,

Subashini.K


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham 
<mark.j.abra...@gmail.com>
Sent: Tuesday, February 28, 2017 9:18 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] ERROR IN BASH SCRIPTING

Hi,

This is not about the logical windows in your system. I'm talking about
your operating system Microsoft Windows. Using cygwin means you have to
handle the intricacies of having two different kinds of operating system
running...

If you used e.g. notepad from Windows to edit the bash file, then the bash
from cygwin won't understand it. The errors look consistent with that. You
can fix that by running the script through dos2unix. Next time, do that, or
use an editor that comes from cygwin.

Be sure you read things like
https://cygwin.com/cygwin-ug-net/using-effectively.html so you understand
your own tools.

Mark

On Tue, Feb 28, 2017 at 11:54 AM Subashini .K <subashi...@hotmail.com>
wrote:

> Hi,
>
>
> Thank you for the reply.
>
>
> WINDOW represents the distance between two identical molecules in
> umbrella sampling method.
>
>
> In order to avoid having 26 different mdp files, we use the bash script
> use  to loop through and run each state .
>
>
> This was developed by WESBARNETT (displayed in the tutorial link)
>
>
> But, I am unable to run the bash script.
>
>
> My question is in which folder the bash script must be placed?
>
>
>
> I use cgywin windows  and notepad ++.
>
>
> Can anyone help?
>
>
> Thanks,
>
> Subashini.K
>
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abra...@gmail.com>
> Sent: Tuesday, February 28, 2017 2:31 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] ERROR IN BASH SCRIPTING
>
> Hi,
>
> Looks like you edited on Windows last. Use dos2unix now, or a proper text
> editor next time ;-)
>
> Mark
>
> On Tue, 28 Feb 2017 08:14 Subashini .K <subashi...@hotmail.com> wrote:
>
> > Hi gromacs users,
> >
> >
> > I use the following run.sh in the working directory of simulations
> >
> >
> > #!/bin/bash
> > set -e
> >
> > for ((i=0;i<27;i++)); do
> >
> > x=$(echo "0.05*$(($i+1))" | bc);
> >
> > sed 's/WINDOW/'$x'/g' mdp/min.mdp > grompp.mdp
> > gmx grompp -o min.$i -pp min.$i -po min.$i -n index.ndx
> > gmx mdrun -deffnm min.$i -pf pullf-min.$i -px pullx-min.$i
> >
> > sed 's/WINDOW/'$x'/g' mdp/min2.mdp > grompp.mdp
> > gmx grompp -o min2.$i -c min.$i -t min.$i -pp min2.$i -po min2.$i
> > -maxwarn 1 -n index.ndx
> > gmx mdrun -deffnm min2.$i -pf pullf-min2.$i -px pullx-min2.$i
> >
> > sed 's/WINDOW/'$x'/g' mdp/eql.mdp > grompp.mdp
> > gmx grompp -o eql.$i -c min2.$i -t min2.$i -pp eql.$i -po eql.$i -n
> > index.ndx
> > gmx mdrun -deffnm eql.$i -pf pullf-eql.$i -px pullx-eql.$i
> >
> > sed 's/WINDOW/'$x'/g' mdp/eql2.mdp > grompp.mdp
> > gmx grompp -o eql2.$i -c eql.$i -t eql.$i -pp eql2.$i -po eql2.$i -n
> > index.ndx
> > gmx mdrun -deffnm eql2.$i -pf pullf-eql2.$i -px pullx-eql2.$i
> >
> > sed 's/WINDOW/'$x'/g' mdp/prd.mdp > grompp.mdp
> > gmx grompp -o prd.$i -c eql2.$i -t eql2.$i -pp prd.$i -po prd.$i -n
> > index.ndx
> > gmx mdrun -deffnm prd.$i -pf pullf-prd.$i -px pullx-prd.$i
> >
> > done
> >
> > However, I get the following error
> >
> >
> >  ./run.sh
> > : invalid option: set: -
> > set: usage: set [-abefhkmnptuvxBCHP] [-o option-name] [--] [arg ...]
> > ./run.sh: line 3: $'\r': command not found
> > ./run.sh: line 4: syntax error near unexpected token `$'do\r''
> > '/run.sh: line 4: `for ((i=0;i<27;i++)); do
> >
> >
> > How to fix it?
> >
> >
> > Thanks,
> >
> > Subashini.K
> >
>
> --

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Re: [gmx-users] ERROR IN BASH SCRIPTING

[Subashini .K]

Hi,


Thank you for the reply.


WINDOW represents the distance between two identical molecules in  umbrella 
sampling method.


In order to avoid having 26 different mdp files, we use the bash script use  to 
loop through and run each state .


This was developed by WESBARNETT (displayed in the tutorial link)


But, I am unable to run the bash script.


My question is in which folder the bash script must be placed?



I use cgywin windows  and notepad ++.


Can anyone help?


Thanks,

Subashini.K




From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham 
<mark.j.abra...@gmail.com>
Sent: Tuesday, February 28, 2017 2:31 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] ERROR IN BASH SCRIPTING

Hi,

Looks like you edited on Windows last. Use dos2unix now, or a proper text
editor next time ;-)

Mark

On Tue, 28 Feb 2017 08:14 Subashini .K <subashi...@hotmail.com> wrote:

> Hi gromacs users,
>
>
> I use the following run.sh in the working directory of simulations
>
>
> #!/bin/bash
> set -e
>
> for ((i=0;i<27;i++)); do
>
> x=$(echo "0.05*$(($i+1))" | bc);
>
> sed 's/WINDOW/'$x'/g' mdp/min.mdp > grompp.mdp
> gmx grompp -o min.$i -pp min.$i -po min.$i -n index.ndx
> gmx mdrun -deffnm min.$i -pf pullf-min.$i -px pullx-min.$i
>
> sed 's/WINDOW/'$x'/g' mdp/min2.mdp > grompp.mdp
> gmx grompp -o min2.$i -c min.$i -t min.$i -pp min2.$i -po min2.$i
> -maxwarn 1 -n index.ndx
> gmx mdrun -deffnm min2.$i -pf pullf-min2.$i -px pullx-min2.$i
>
> sed 's/WINDOW/'$x'/g' mdp/eql.mdp > grompp.mdp
> gmx grompp -o eql.$i -c min2.$i -t min2.$i -pp eql.$i -po eql.$i -n
> index.ndx
> gmx mdrun -deffnm eql.$i -pf pullf-eql.$i -px pullx-eql.$i
>
> sed 's/WINDOW/'$x'/g' mdp/eql2.mdp > grompp.mdp
> gmx grompp -o eql2.$i -c eql.$i -t eql.$i -pp eql2.$i -po eql2.$i -n
> index.ndx
> gmx mdrun -deffnm eql2.$i -pf pullf-eql2.$i -px pullx-eql2.$i
>
> sed 's/WINDOW/'$x'/g' mdp/prd.mdp > grompp.mdp
> gmx grompp -o prd.$i -c eql2.$i -t eql2.$i -pp prd.$i -po prd.$i -n
> index.ndx
> gmx mdrun -deffnm prd.$i -pf pullf-prd.$i -px pullx-prd.$i
>
> done
>
> However, I get the following error
>
>
>  ./run.sh
> : invalid option: set: -
> set: usage: set [-abefhkmnptuvxBCHP] [-o option-name] [--] [arg ...]
> ./run.sh: line 3: $'\r': command not found
> ./run.sh: line 4: syntax error near unexpected token `$'do\r''
> '/run.sh: line 4: `for ((i=0;i<27;i++)); do
>
>
> How to fix it?
>
>
> Thanks,
>
> Subashini.K
>

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[gmx-users] ERROR IN BASH SCRIPTING

[Subashini .K]

Hi gromacs users,


I use the following run.sh in the working directory of simulations


#!/bin/bash
set -e

for ((i=0;i<27;i++)); do

x=$(echo "0.05*$(($i+1))" | bc);

sed 's/WINDOW/'$x'/g' mdp/min.mdp > grompp.mdp
gmx grompp -o min.$i -pp min.$i -po min.$i -n index.ndx
gmx mdrun -deffnm min.$i -pf pullf-min.$i -px pullx-min.$i

sed 's/WINDOW/'$x'/g' mdp/min2.mdp > grompp.mdp
gmx grompp -o min2.$i -c min.$i -t min.$i -pp min2.$i -po min2.$i -maxwarn 
1 -n index.ndx
gmx mdrun -deffnm min2.$i -pf pullf-min2.$i -px pullx-min2.$i

sed 's/WINDOW/'$x'/g' mdp/eql.mdp > grompp.mdp
gmx grompp -o eql.$i -c min2.$i -t min2.$i -pp eql.$i -po eql.$i -n 
index.ndx
gmx mdrun -deffnm eql.$i -pf pullf-eql.$i -px pullx-eql.$i

sed 's/WINDOW/'$x'/g' mdp/eql2.mdp > grompp.mdp
gmx grompp -o eql2.$i -c eql.$i -t eql.$i -pp eql2.$i -po eql2.$i -n 
index.ndx
gmx mdrun -deffnm eql2.$i -pf pullf-eql2.$i -px pullx-eql2.$i

sed 's/WINDOW/'$x'/g' mdp/prd.mdp > grompp.mdp
gmx grompp -o prd.$i -c eql2.$i -t eql2.$i -pp prd.$i -po prd.$i -n 
index.ndx
gmx mdrun -deffnm prd.$i -pf pullf-prd.$i -px pullx-prd.$i

done

However, I get the following error


 ./run.sh
: invalid option: set: -
set: usage: set [-abefhkmnptuvxBCHP] [-o option-name] [--] [arg ...]
./run.sh: line 3: $'\r': command not found
./run.sh: line 4: syntax error near unexpected token `$'do\r''
'/run.sh: line 4: `for ((i=0;i<27;i++)); do


How to fix it?


Thanks,

Subashini.K

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[gmx-users] TOPOLBUILD 1.3

[Subashini .K]

Hi gromacs users,


I want to use oplsaa force field for my organic compound.


Can anyone tell me how to install topolbuild 1.3 and thereby generate .GRO, 
.ITP and .TOP with opls-aa parameter incorporated in it?


Thanks,

Subashini.K
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Re: [gmx-users] deformation in simulation

[Subashini .K]

Many tutorials suggest to run two equilibrations and then production file.


At first, run a restrained equilibrium.


Then non-restrained equilibrium followed by production file.


Do not know the aim of your simulations.


Hope this answer helps.


Thanks,

Subashini.K


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of RAHUL SURESH 

Sent: Thursday, February 23, 2017 12:23 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] deformation in simulation

Simulating a protein with 100residues for 200ns doesn't show any stability.
There are some deformation(long-bonds) in the structure throughout the
process. Why is that so? Can I choose any stable structure in between these
200ns, for example say 176ns. Or is there any other way to make them work
good.I need your valuable suggestions

--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] UMBRELLA SAMPLING

[Subashini .K]

Hi gromacs users,



I want to calculate the binding energy (ΔGbind) using umbrella sampling method 
(between protein and ligand which is solvated in water)


How to custom index groups for the pulling simulation?


The protein under consideration has only one chain A.


Thanks,

Subashini.K

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[gmx-users] PROTEIN-LIGAND SIMULATION

[Subashini .K]

Hi gromacs users,


In order to calculate binding energy of single protein inhibitor complex 
through simulations, how long should we run the calculations?


Is 2ns sufficient?


How to obtain results and plot time (in ps) along x-axis and binding energy 
(kJ/mol)along y-axis?


Had completed two equilibration phases (NVT and NPT)and then used the command 
for production MD (for 2ns).


Can someone help?


Thanks,

Subashini.K
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Re: [gmx-users] DETECTING HYDROGEN BONDS

[Subashini .K]

Thank you very much for the reply


Wanted to know what the third column represents?


The header was


# gmx hbond is part of G R O M A C S:
# # Glycine aRginine prOline Methionine Alanine Cystine Serine #
@title "Hydrogen Bonds"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy @ view 0.15, 0.15, 0.75, 0.85
@ legend on @ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"

Through molecular docking had obtained hydrogen bonding with GLU 387 AND GLU 389

Wish to ascertain them through simulations too. How to do it?

Thanks,
Subashini.K






From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Alex 
<nedoma...@gmail.com>
Sent: Saturday, February 11, 2017 1:45 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] DETECTING HYDROGEN BONDS

Not sure what you mean by "interpret these numbers," except that now we
know that your simulation was 2 ns long.  The xvg file contains a
header, which describes what each column is. If I recall correctly, the
second column is the number of hbonds according to the default search
cutoff. The first column is your simulated time in ps.

Alex


On 2/11/2017 1:00 AM, Subashini .K wrote:
> Hi gromacs users,
>
>
> After protein ligand simulations, gave the following command to detect 
> hydrogen bond
>
>
> gmx hbond -f npt.trr -s npt.tpr -num hbond.xvg
>
> After selecting protein and ligand
>
>
> Obtained the following result
>
>
> I am a beginner. Could someone help me  to interpret these numbers? The 
> simulation was done for 2 ns
>
>
>
>  0   2   1
>
>100   2   1
>
> 200   1   0
>
> 300   1   0
>
> 400   1   0
>
> 500   1   0
>
> 600   1   0
>
>700   1   0
>
>800   0   0
>
>900   1   0
>
> 1000   1   0
>
>  1100   1   0
>
>   1200   1   0
>
>   1300   0   2
>
>  1400   1   0
>
>   1500   1   0
>
>   1600   1   0
>
>1700   1   0
>
>   1800   0   1
>
>1900   1   0
>
>   2000   1   0
>
>
> Thanks,
>
> Subashini.K


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[gmx-users] DETECTING HYDROGEN BONDS

[Subashini .K]

Hi gromacs users,


After protein ligand simulations, gave the following command to detect hydrogen 
bond


gmx hbond -f npt.trr -s npt.tpr -num hbond.xvg

After selecting protein and ligand


Obtained the following result


I am a beginner. Could someone help me  to interpret these numbers? The 
simulation was done for 2 ns



0   2   1

  100   2   1

   200   1   0

   300   1   0

   400   1   0

   500   1   0

   600   1   0

  700   1   0

  800   0   0

  900   1   0

   1000   1   0

1100   1   0

 1200   1   0

 1300   0   2

1400   1   0

 1500   1   0

 1600   1   0

  1700   1   0

 1800   0   1

  1900   1   0

 2000   1   0


Thanks,

Subashini.K
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[gmx-users] ANALYSING PROTEIN LIGAND SIMULATIONS

[Subashini .K]

Hi gromacs users,


Have completed protein ligand simulations for 2 ns.


How to view the position fluctuations of the ligand inside the protein and 
observe stable binding modes?


How to extract useful information post simulations?


Thanks,

Subashini.K


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Re: [gmx-users] Radial distribution function for larger distances

[Subashini .K]

Hi,


Thank you for the reply.


I got RDF for distances up to 1.772 angstrom (in x-axis) using the code 
mentioned.


Can we get it for 15 angstrom?


What should be done?


Thanks,

Subashini.K


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Christopher 
Neale <chris.ne...@alum.utoronto.ca>
Sent: Wednesday, February 8, 2017 10:44 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Radial distribution function for larger distances

It's unclear what your issue is. I presume you are concerned that the rdf might 
not be valid at distances longer than your cutoff? In that case, adding 
dispersion correction might be something to think about, but then again that 
will depend on the force field and the system too. Unless I'm missing something 
you'll likely need to describe precisely what your problem is to get any useful 
suggestions.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Subashini .K 
<subashi...@hotmail.com>
Sent: 08 February 2017 00:08:57
To: gmx-us...@gromacs.org
Subject: [gmx-users] Radial distribution function for larger distances

Hi Gromacs users,


How to calculate RDF for larger distances, say 15 angstrom using the following 
code. In which line should we focus to make changes?


Can someone help?


integrator   = md
dt   = 0.002 ; 2 fs
nsteps   = 500   ; 10.0 ns

nstenergy= 5000
nstlog   = 5000
nstxout-compressed   = 2000

continuation = yes
constraint-algorithm = lincs
constraints  = h-bonds

cutoff-scheme= Verlet

coulombtype  = PME
rcoulomb = 1.0

vdwtype  = Cut-off
rvdw = 1.0
DispCorr = EnerPres

tcoupl   = Nose-Hoover
tc-grps  = System
tau-t= 2.0
ref-t= 298.15
nhchainlength= 1

pcoupl   = Parrinello-Rahman
tau_p= 2.0
compressibility  = 4.46e-5
ref_p= 1.0

Thanks,
Subashini.K


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[gmx-users] Radial distribution function for larger distances

[Subashini .K]

Hi Gromacs users,


How to calculate RDF for larger distances, say 15 angstrom using the following 
code. In which line should we focus to make changes?


Can someone help?


integrator   = md
dt   = 0.002 ; 2 fs
nsteps   = 500   ; 10.0 ns

nstenergy= 5000
nstlog   = 5000
nstxout-compressed   = 2000

continuation = yes
constraint-algorithm = lincs
constraints  = h-bonds

cutoff-scheme= Verlet

coulombtype  = PME
rcoulomb = 1.0

vdwtype  = Cut-off
rvdw = 1.0
DispCorr = EnerPres

tcoupl   = Nose-Hoover
tc-grps  = System
tau-t= 2.0
ref-t= 298.15
nhchainlength= 1

pcoupl   = Parrinello-Rahman
tau_p= 2.0
compressibility  = 4.46e-5
ref_p= 1.0

Thanks,
Subashini.K

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Re: [gmx-users] INDEX

[Subashini .K]

Hi,


Lot of thanks.

I'll implement it in the command line.


Thanks,

Subashini.K



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Erik Marklund 
<erik.markl...@kemi.uu.se>
Sent: Monday, February 6, 2017 6:07 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] INDEX

Dear Subashini,

You forgot to provide trjconv with the index file you created. Try gmx trjconv 
-n your_index_file.ndx …

Kind regards,
Erik
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 6 Feb 2017, at 13:06, Subashini .K 
<subashi...@hotmail.com<mailto:subashi...@hotmail.com>> wrote:

Hi gromacs users,


I want to visualize the results of simulations using the command


gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb


Wish to see Protein and ligand simulations together in the pdb file.


But, when the command is given, we can either select protein group or ligand 
group


Before this was done,


The following commands were given

(1)  gmx make_ndx -f em.gro

In this step, group No 22 was created namely Protein-ligand

(2)genrestr -f em.gro -n index.ndx -fc 500 500 500

(3) gmx grompp -f nvt.mdp -c em.gro -p complex_GMX.top -n index.ndx -o nvt.tpr

(4) gmx mdrun -deffnm nvt


However, despite typing make_ndx 1|13 (Protein-ligand), it is not reflected in 
the movie.pdb file.


What to do?

Can someone help?


Thanks,

Subashini.K


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[gmx-users] INDEX

[Subashini .K]

Hi gromacs users,


I want to visualize the results of simulations using the command


gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb


Wish to see Protein and ligand simulations together in the pdb file.


But, when the command is given, we can either select protein group or ligand 
group


Before this was done,


The following commands were given

(1)  gmx make_ndx -f em.gro

In this step, group No 22 was created namely Protein-ligand

(2)genrestr -f em.gro -n index.ndx -fc 500 500 500

(3) gmx grompp -f nvt.mdp -c em.gro -p complex_GMX.top -n index.ndx -o nvt.tpr

(4) gmx mdrun -deffnm nvt


However, despite typing make_ndx 1|13 (Protein-ligand), it is not reflected in 
the movie.pdb file.


What to do?

Can someone help?


Thanks,

Subashini.K


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[gmx-users] PROTEIN LIGAND SIMULATION DYNAMICS

[Subashini .K]

Hi Gromacs users,


I am new to simulation dynamics.


On what basis do we add  water molecules to the protein ligand complex?


Should we ensure that the system is fully solvated?


Or, can we consider simulation without solvent (water molecules)?


Thanks,

Subashini.K



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[gmx-users] VISUALIZING PROTEIN FOLDING

[Subashini .K]

Hi gromacs users,


Through NVT equilibration, had obtained nvt.gro and nvt.trr.

Are these files sufficient to visualize protein folding?


What option in VMD has to be explored to observe protein folding?


Thanks,
Subashini.K


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[gmx-users] PROTEIN FOLDING IN GROMACS

[Subashini .K]

Hi gromacs users,


What are the steps for simulation to observe protein folding in gromacs?


Thanks,

Subashini.K

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Re: [gmx-users] REGARDING TOPOLOGY FILE

[Subashini .K]

Thank you for the reply.


Have detected the actual problem and fixed it.


The atom numbering is different in mol2 file and hence in the acpype generated 
file. Nothing wrong in it.


But, in the gro file, apart from two hydrogen atoms and one oxygen atom, there 
was "EPW".


Hence, had to delete it (which was 415)


Now the .top and .gro match each other.


Simulations are fine.




From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Amir Zeb 
<zebami...@gmail.com>
Sent: Thursday, January 19, 2017 12:40 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE

can you please recognize that two extra atoms generated by acepype??

On Jan 19, 2017 4:00 PM, "Subashini .K" <subashi...@hotmail.com> wrote:

> Thank you very much for the reply.
>
>
> Actually, tried converting the ligand alone to .top and .gro file.
>
>
> The ligand contains only 29 atoms.
>
>
> But, in the top and gro generated by acpype it shows 31 atoms.
>
>
> There lies the problem.
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Amir Zeb <
> zebami...@gmail.com>
> Sent: Thursday, January 19, 2017 12:24 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
>
> Hello
> review the number of atoms in gro file and top file
> also check that the 2nd line in gro file showing the total number of atoms
> should be in parallel with all the atoms existed in the gro file
> this way you may solve the problem
> good luck
>
> On Jan 19, 2017 3:20 PM, "Subashini .K" <subashi...@hotmail.com> wrote:
>
> > Hi,
> >
> >
> >
> > Thank you for the reply. As I said earlier, there is one ligand molecule
> > surrounded by many water molecules (680)
> >
> >
> > Here, it is like this
> >
> >
> > [ molecules ]
> > ; Compoundnmols
> >  ligand   1
> >  WAT  680
> >
> >
> > 680 seems to be a correct number. Because, it was computed as follows,
> > using tleap of AMBER TOOLS 15:
> >
> >
> > solvateBox LIG TIP4PBOX 10.0
> >  Solute vdw bounding box:  9.963 8.173 7.953
> >   Total bounding box for atom centers:  29.963 28.173 27.953
> >   Solvent unit box: 18.860 18.867 18.860
> >   Total vdw box size:   33.150 30.999 31.097 angstroms.
> >   Volume: 31955.384 A^3
> >   Total mass 12429.154 amu,  Density 0.646 g/cc
> >   Added 680 residues.
> >
> > Still, there is an error.
> >
> >
> > 
> > 
> > 
> > -
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of tasneem
> > kausar <tasneemkausa...@gmail.com>
> > Sent: Thursday, January 19, 2017 11:04 AM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
> >
> > The error show that the number of atoms in topology file and gro file
> does
> > not match
> > In last line of topology file define the ligand molecule.
> > here is the exapmle
> >
> > [ molecules ]
> > ; Compound#mols
> > Protein_chain_A 1
> > DRG 1
> >
> >
> >
> >
> > On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K <subashi...@hotmail.com>
> > wrote:
> >
> > > Hi gromacs users,
> > >
> > >
> > > Had taken one organic molecule (ligand) and many water molecules using
> > > tleap of Amber tools 15.
> > >
> > >
> > > Then generated .top and .gro file using acpype by the command,
> > >
> > > acpype -p com_solvated.top -x com_solvated.crd -b ligand
> > >
> > >
> > > However, while using the same for gromacs, obtained the following error
> > >
> > >
> > > number of coordinates in coordinate file (conf.gro, 2751)
> > >  does not match topology (topol.top, 2071)
> > >
> > > How to fix this error?
> > >
> > > Thanks,
> > > Subashini.K
> >
> > --
>
> --
> Gromacs Users mailing list
>

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Re: [gmx-users] REGARDING TOPOLOGY FILE

[Subashini .K]

Thank you very much for the reply.


Actually, tried converting the ligand alone to .top and .gro file.


The ligand contains only 29 atoms.


But, in the top and gro generated by acpype it shows 31 atoms.


There lies the problem.



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Amir Zeb 
<zebami...@gmail.com>
Sent: Thursday, January 19, 2017 12:24 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE

Hello
review the number of atoms in gro file and top file
also check that the 2nd line in gro file showing the total number of atoms
should be in parallel with all the atoms existed in the gro file
this way you may solve the problem
good luck

On Jan 19, 2017 3:20 PM, "Subashini .K" <subashi...@hotmail.com> wrote:

> Hi,
>
>
>
> Thank you for the reply. As I said earlier, there is one ligand molecule
> surrounded by many water molecules (680)
>
>
> Here, it is like this
>
>
> [ molecules ]
> ; Compoundnmols
>  ligand   1
>  WAT  680
>
>
> 680 seems to be a correct number. Because, it was computed as follows,
> using tleap of AMBER TOOLS 15:
>
>
> solvateBox LIG TIP4PBOX 10.0
>  Solute vdw bounding box:  9.963 8.173 7.953
>   Total bounding box for atom centers:  29.963 28.173 27.953
>   Solvent unit box: 18.860 18.867 18.860
>   Total vdw box size:   33.150 30.999 31.097 angstroms.
>   Volume: 31955.384 A^3
>   Total mass 12429.154 amu,  Density 0.646 g/cc
>   Added 680 residues.
>
> Still, there is an error.
>
>
> 
> 
> 
> -
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of tasneem
> kausar <tasneemkausa...@gmail.com>
> Sent: Thursday, January 19, 2017 11:04 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE
>
> The error show that the number of atoms in topology file and gro file does
> not match
> In last line of topology file define the ligand molecule.
> here is the exapmle
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> DRG 1
>
>
>
>
> On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K <subashi...@hotmail.com>
> wrote:
>
> > Hi gromacs users,
> >
> >
> > Had taken one organic molecule (ligand) and many water molecules using
> > tleap of Amber tools 15.
> >
> >
> > Then generated .top and .gro file using acpype by the command,
> >
> > acpype -p com_solvated.top -x com_solvated.crd -b ligand
> >
> >
> > However, while using the same for gromacs, obtained the following error
> >
> >
> > number of coordinates in coordinate file (conf.gro, 2751)
> >  does not match topology (topol.top, 2071)
> >
> > How to fix this error?
> >
> > Thanks,
> > Subashini.K
>
> --

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Re: [gmx-users] REGARDING TOPOLOGY FILE

[Subashini .K]

Hi,



Thank you for the reply. As I said earlier, there is one ligand molecule 
surrounded by many water molecules (680)


Here, it is like this


[ molecules ]
; Compoundnmols
 ligand   1
 WAT  680


680 seems to be a correct number. Because, it was computed as follows, using 
tleap of AMBER TOOLS 15:


solvateBox LIG TIP4PBOX 10.0
 Solute vdw bounding box:  9.963 8.173 7.953
  Total bounding box for atom centers:  29.963 28.173 27.953
  Solvent unit box: 18.860 18.867 18.860
  Total vdw box size:   33.150 30.999 31.097 angstroms.
  Volume: 31955.384 A^3
  Total mass 12429.154 amu,  Density 0.646 g/cc
  Added 680 residues.

Still, there is an error.


-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of tasneem kausar 
<tasneemkausa...@gmail.com>
Sent: Thursday, January 19, 2017 11:04 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REGARDING TOPOLOGY FILE

The error show that the number of atoms in topology file and gro file does
not match
In last line of topology file define the ligand molecule.
here is the exapmle

[ molecules ]
; Compound#mols
Protein_chain_A 1
DRG 1




On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K <subashi...@hotmail.com>
wrote:

> Hi gromacs users,
>
>
> Had taken one organic molecule (ligand) and many water molecules using
> tleap of Amber tools 15.
>
>
> Then generated .top and .gro file using acpype by the command,
>
> acpype -p com_solvated.top -x com_solvated.crd -b ligand
>
>
> However, while using the same for gromacs, obtained the following error
>
>
> number of coordinates in coordinate file (conf.gro, 2751)
>  does not match topology (topol.top, 2071)
>
> How to fix this error?
>
> Thanks,
> Subashini.K

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[gmx-users] REGARDING TOPOLOGY FILE

[Subashini .K]

Hi gromacs users,


Had taken one organic molecule (ligand) and many water molecules using tleap of 
Amber tools 15.


Then generated .top and .gro file using acpype by the command,

acpype -p com_solvated.top -x com_solvated.crd -b ligand


However, while using the same for gromacs, obtained the following error


number of coordinates in coordinate file (conf.gro, 2751)
 does not match topology (topol.top, 2071)

How to fix this error?

Thanks,
Subashini.K

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[gmx-users] CLARIFICATION IN RESIDUE TOPOLOGY FILE

[Subashini .K]

Hi gromacs users,


While preparing the .rtp file, what does the third and fourth column describe?

; Methane
[ CH4 ]
[ atoms ]


C  opls_138-0.240 1

H1 opls_140 0.060 1

H2 opls_140 0.060 1

H3 opls_140 0.060 1

H4 opls_140 0.060 1


Does the number -0.240 indicate the charge of Carbon? Does it indicate Mulliken 
charge/electrostatic potential charge? How to calculate it for any arbitrary 
organic molecule?


Thanks,

Subashini.K





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[gmx-users] PREPARING THE RESIDUE TOPOLOGY FILE

[Subashini .K]

Hi,



I am learning to prepare the residue topology file (.rtp file) .


While preparing the file, what does the third and fourth column describe?


This is the example of methane. What do the numbers -0.240 and 1 convey? 
Similarly 0.060 and 1?


[ bondedtypes ]
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 3 1 1 3 1 0


; Methane
[ CH4 ]
[ atoms ]


C  opls_138-0.240 1

H1 opls_140 0.060 1

H2 opls_140 0.060 1

H3 opls_140 0.060 1

H4 opls_140 0.060 1



Please explain.


Thanks,

Subashini.K



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Re: [gmx-users] converting pdb file to gromacs input file

[Subashini .K]

It says, RESIDUE NOT FOUND in residue topology database


For example in methane, the example was



COMPNDMETHANE
AUTHORGENERATED BY OPEN BABEL 2.3.2
HETATM1  C   CH4 1  -0.370   0.900   0.000  1.00  0.00   C
HETATM2  H1  CH4 1   0.700   0.900   0.000  1.00  0.00   H
HETATM3  H2  CH4 1  -0.727   0.122   0.643  1.00  0.00   H
HETATM4  H3  CH4 1  -0.727   0.731  -0.995  1.00  0.00   H
HETATM5  H4  CH4 1  -0.727   1.845   0.351  1.00  0.00   H
END


What does CH4 mean here?


Then, should we mention the hybridization of each and every atom?



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sotirios 
Dionysios I. Papadatos <si.papada...@edu.cut.ac.cy>
Sent: Saturday, January 14, 2017 4:06 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] converting pdb file to gromacs input file

In pdb2gmx you give as an input the filename.pdb. This should do the trick. But 
I think there is something else that you truly need. Maybe you need some more 
info on how to add a hetatm in an existing force field.?


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Subashini .K 
<subashi...@hotmail.com>
Sent: Saturday, January 14, 2017 12:04:40 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] converting pdb file to gromacs input file

Hi gromacs users,


I am a new gromacs user.


I wanted to generate a .gro, .itp, .conf file using the command


$ gmx pdb2gmx -f lig.pdb


However, the pdb file must be in the required format.

What should we type instead of LIG corresponding to each and every atom?


This is an example file of phenylcyclohexane.

Please tell me how to proceed further?


COMPNDPhenylcyclohexane
AUTHORGENERATED BY OPEN BABEL 2.3.2
HETATM1  C   LIG 1  -2.801   1.177   0.180  1.00  0.00   C
HETATM2  C   LIG 1  -1.406   1.177   0.180  1.00  0.00   C
HETATM3  C   LIG 1  -0.708   2.371   0.000  1.00  0.00   C
HETATM4  C   LIG 1  -1.405   3.566  -0.181  1.00  0.00   C
HETATM5  C   LIG 1  -2.800   3.566  -0.181  1.00  0.00   C
HETATM6  C   LIG 1  -3.498   2.372  -0.001  1.00  0.00   C
HETATM7  H   LIG 1  -3.350   0.236   0.322  1.00  0.00   H
HETATM8  H   LIG 1  -0.856   0.235   0.323  1.00  0.00   H
HETATM9  H   LIG 1  -0.855   4.508  -0.323  1.00  0.00   H
HETATM   10  H   LIG 1  -3.350   4.508  -0.324  1.00  0.00   H
HETATM   11  H   LIG 1  -4.598   2.372  -0.001  1.00  0.00   H
HETATM   12  C   LIG 1   0.832   2.372   0.001  1.00  0.00   C
HETATM   13  C   LIG 1   1.339   1.686   1.253  1.00  0.00   C
HETATM   14  C   LIG 1   1.341   1.681  -1.248  1.00  0.00   C
HETATM   15  H   LIG 1   1.170   3.441  -0.001  1.00  0.00   H
HETATM   16  C   LIG 1   2.852   1.589   1.256  1.00  0.00   C
HETATM   17  H   LIG 1   0.900   0.655   1.317  1.00  0.00   H
HETATM   18  H   LIG 1   0.998   2.254   2.157  1.00  0.00   H
HETATM   19  C   LIG 1   2.853   1.585  -1.246  1.00  0.00   C
HETATM   20  H   LIG 1   0.902   0.650  -1.309  1.00  0.00   H
HETATM   21  H   LIG 1   1.002   2.245  -2.155  1.00  0.00   H
HETATM   22  C   LIG 1   3.361   0.900   0.006  1.00  0.00   C
HETATM   23  H   LIG 1   3.190   1.023   2.162  1.00  0.00   H
HETATM   24  H   LIG 1   3.291   2.620   1.318  1.00  0.00   H
HETATM   25  H   LIG 1   3.194   1.016  -2.150  1.00  0.00   H
HETATM   26  H   LIG 1   3.291   2.615  -1.311  1.00  0.00   H
HETATM   27  H   LIG 1   4.482   0.903   0.007  1.00  0.00   H
HETATM   28  H   LIG 1   3.027  -0.170   0.008  1.00  0.00   H

Thanks,
Subashini.K

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[gmx-users] converting pdb file to gromacs input file

[Subashini .K]

Hi gromacs users,


I am a new gromacs user.


I wanted to generate a .gro, .itp, .conf file using the command


$ gmx pdb2gmx -f lig.pdb


However, the pdb file must be in the required format.

What should we type instead of LIG corresponding to each and every atom?


This is an example file of phenylcyclohexane.

Please tell me how to proceed further?


COMPNDPhenylcyclohexane
AUTHORGENERATED BY OPEN BABEL 2.3.2
HETATM1  C   LIG 1  -2.801   1.177   0.180  1.00  0.00   C
HETATM2  C   LIG 1  -1.406   1.177   0.180  1.00  0.00   C
HETATM3  C   LIG 1  -0.708   2.371   0.000  1.00  0.00   C
HETATM4  C   LIG 1  -1.405   3.566  -0.181  1.00  0.00   C
HETATM5  C   LIG 1  -2.800   3.566  -0.181  1.00  0.00   C
HETATM6  C   LIG 1  -3.498   2.372  -0.001  1.00  0.00   C
HETATM7  H   LIG 1  -3.350   0.236   0.322  1.00  0.00   H
HETATM8  H   LIG 1  -0.856   0.235   0.323  1.00  0.00   H
HETATM9  H   LIG 1  -0.855   4.508  -0.323  1.00  0.00   H
HETATM   10  H   LIG 1  -3.350   4.508  -0.324  1.00  0.00   H
HETATM   11  H   LIG 1  -4.598   2.372  -0.001  1.00  0.00   H
HETATM   12  C   LIG 1   0.832   2.372   0.001  1.00  0.00   C
HETATM   13  C   LIG 1   1.339   1.686   1.253  1.00  0.00   C
HETATM   14  C   LIG 1   1.341   1.681  -1.248  1.00  0.00   C
HETATM   15  H   LIG 1   1.170   3.441  -0.001  1.00  0.00   H
HETATM   16  C   LIG 1   2.852   1.589   1.256  1.00  0.00   C
HETATM   17  H   LIG 1   0.900   0.655   1.317  1.00  0.00   H
HETATM   18  H   LIG 1   0.998   2.254   2.157  1.00  0.00   H
HETATM   19  C   LIG 1   2.853   1.585  -1.246  1.00  0.00   C
HETATM   20  H   LIG 1   0.902   0.650  -1.309  1.00  0.00   H
HETATM   21  H   LIG 1   1.002   2.245  -2.155  1.00  0.00   H
HETATM   22  C   LIG 1   3.361   0.900   0.006  1.00  0.00   C
HETATM   23  H   LIG 1   3.190   1.023   2.162  1.00  0.00   H
HETATM   24  H   LIG 1   3.291   2.620   1.318  1.00  0.00   H
HETATM   25  H   LIG 1   3.194   1.016  -2.150  1.00  0.00   H
HETATM   26  H   LIG 1   3.291   2.615  -1.311  1.00  0.00   H
HETATM   27  H   LIG 1   4.482   0.903   0.007  1.00  0.00   H
HETATM   28  H   LIG 1   3.027  -0.170   0.008  1.00  0.00   H

Thanks,
Subashini.K

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[gmx-users] G_ENERGY COMMAND

[Subashini .K]

Hi gromacs users,


I am using gromacs in windows 7, 64 bit.


When the following command was given,


gmx g_energy -f ener.part0001.edr -o vol.xvg



the error was


GROMACS:  gmx, VERSION 5.1.1
Executable:   /usr/local/gromacs/bin/gmx.exe
Data prefix:  /usr/local/gromacs
Command line:
  gmx g_energy -f ener.part0001.edr -o vol.xvg

---
Program: gmx, VERSION 5.1.1
Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 376)
Function:gmx::CommandLineModuleInterface* 
gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*,
 int*, char***)

Error in user input:
'g_energy' is not a GROMACS command.

How to fix it? What is the correct command?


Thanks,
Subashini.K

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[gmx-users] REGARDING PROTEIN LIGAND SIMULATION

[Subashini .K]

Hi gromacs users,


I am working on protein-ligand simulation..The commands were given in the 
following order

(1)


source leaprc.ff14SB
loadAmberParams frcmod.tip4pew
loadAmberParams frcmod.ionsjc_tip4pew
source leaprc.gaff
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG
receptor = loadPDB rec_final.pdb
complex = combine {receptor LIG}
set default PBRadii mbondi2
saveAmberParm LIG LIG.top LIG.crd
receptor = loadPDB rec_final.pdb
saveAmberParm receptor rec.top rec.crd
saveAmberParm complex com.top com.crd
savepdb complex complex_gas.pdb
charge complex
addIons2 complex Na+ 0
solvateBox complex TIP4PBOX 10.0
saveAmberParm complex com_solvated.top com_solvated.crd
savepdb complex com_solvated.pdb
quit

(2)

acpype -p com_solvated.top -x com_solvated.crd -b complex


After the following grompp command,

(3)
 gmx grompp -f em.mdp -c complex_GMX.gro -p complex_GMX.top -o em

where
#em.mdp

; to test
; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
; mdrun -v -deffnm em
 #Grompp minimization
integrator = steep
nsteps = 500
nstlist = 10
energy-grps = receptor LIG
cutoff-scheme = verlet
vdw-type = cut-off
rvdw = 1.0
coulombtype = pme
rcoulomb = 1.0

The fatal error was


(1) Group receptor referenced in the .mdp file was not found in the index file. 
Group names must match either [moleculetype] names or custom index groupnames, 
in which case you must supply an index file to the '-n' option
of grompp.


and

NOTE 1 [file complex_GMX.top, line 5]:
  System has non-zero total charge: -0.000243
  Total charge should normally be an integer.

How can I fix the error? What commands should be given? Please help.

The protein was rec.pdb and ligand was lig.mol2

Where to spot the names in the .GRO file for energy-grps




Thanks,
Subashini.K

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Re: [gmx-users] gromacs in cgywin

[Subashini .K]

Hi,



Had included a few more lines in .mdp file and now it is working well.


Thanks,

Subashini.K


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of liming_52 
<liming...@163.com>
Sent: Wednesday, January 11, 2017 1:59 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs in cgywin

Delete the ";", and it maybe bring some surprise. For example, run "grompp -f 
em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v" or "mdrun -v -deffnm em".





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China



At 2017-01-11 16:24:16, "Subashini .K" <subashi...@hotmail.com> wrote:
>Hi,
>
>
>I have installed gromacs in cgywin.
>
>I want to run these commands
>
>
>#em.mdp
>; to test
>; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
>; mdrun -v -deffnm em
>
>
>I had sourced gmrx before typing these commands.
>
>source /usr/local/gromacs/bin/GMXRC
>
>
>But, it says,   -bash: syntax error near unexpected token `;'
>
>
>How to rectify it?
>
>
>Thanks,
>
>Subashini.K
>
>--
>Gromacs Users mailing list
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[gmx-users] gromacs in cgywin

[Subashini .K]

Hi,


I have installed gromacs in cgywin.

I want to run these commands


#em.mdp
; to test
; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
; mdrun -v -deffnm em


I had sourced gmrx before typing these commands.

source /usr/local/gromacs/bin/GMXRC


But, it says,   -bash: syntax error near unexpected token `;'


How to rectify it?


Thanks,

Subashini.K

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[gmx-users] GROMACS IN CGYWIN

[Subashini .K]

Hi,


In cgywin, I typed this command


 source /usr/local/gromacs/bin/GMXRC

After that, cd  /way-to-the-required-directory/was given


But, when


; test

is given, it says,


-bash: syntax error near unexpected token `;'


Gromacs was installed following the instructions in this website

https://winmostar.com/en/gmx4wm_en_win.html


How to rectify it? Please help.

Thanks,
Subashini.K



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham 
<mark.j.abra...@gmail.com>
Sent: Wednesday, January 11, 2017 12:30 AM
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] ENERGY MINIMIZATION

Hi,

In a cygwin terminal, having source'd GMXRC (see the install guide), just
like you need to do under Linux.

Mark

On Tue, Jan 10, 2017 at 7:29 PM Subashini .K <subashi...@hotmail.com> wrote:

> Hi Gromacs users,
>
>
> I have installed gromacs in windows 7, 64 bit using cgywin.
>
>
> I want to use the em.mdp file to grompp and generate a .tpr file.
>
>
> In which terminal should the following commands be executed?
>
>
> ; to test
> ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
> ; mdrun -v -deffnm em
>
> Can someone tell me?
>
>
> Thanks,
>
> Subashini.K
>
>
> --
> 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] ENERGY MINIMIZATION

[Subashini .K]

Hi Gromacs users,


I have installed gromacs in windows 7, 64 bit using cgywin.


I want to use the em.mdp file to grompp and generate a .tpr file.


In which terminal should the following commands be executed?


; to test
; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
; mdrun -v -deffnm em

Can someone tell me?


Thanks,

Subashini.K


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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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[gmx-users] Error in leaprc.ff14SB (Amber14)

[Subashini .K]

Hi Gromacs users,



While using the tleap of AmberTools 15,


we give the following command


 source /home/admin/amber14/dat/leap/cmd/leaprc.ff14SB




However, the following error is shown in cgywin command prompt


-bash: logFile: command not found
-bash: addAtomTypes: command not found
-bash: /home/admin/amber14/dat/leap/cmd/leaprc.ff14SB: line 209: syntax error: 
unexpected end of file


How to fix it?

Thanks,
Subashini.K



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[gmx-users] HOW TO RUN GROMACS IN WINDOWS 7

[Subashini .K]

Hi Gromacs users,


I am new to Gromacs. Have installed it in windows 7.

Had followed the instructions this website 
https://winmostar.com/en/gmx4wm_en_win.html


How to run a test file through cygwin? Can someone help?


Thanks,

Subashini.K
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