[gmx-users] dna-simualtions with gromacs

[amna khan]

hi .

i want to simulate the DNA in water, all gromacs  force fields does not
support DNA . so i chose the amber force fields from Gromacs package,

i want to ask , are all remaining steps same for DNA simulations like the
lyzome example ?

plase help me

i have done till this step

pdb2gmx -ff amber99sb -f DNAAmber.pdb -o DNA2.pdb -p DNA.top -water spce
-ignh

editconf -bt octahedron -f  DNA2.pdb -o Complex.pdb -d 1.0
genbox -cp Complex.pdb -cs spc216.gro -o Complex_b4ion.pdb -p DNA.top

grompp -f em.mdp -c Complex_b4ion.pdb -p DNA.top -o Complex_b4ion.tpr

genion -s Complex_b4ion.tpr -o Complex_b4em.pdb –nname Na –nn 8 –g
trp_ion.log

rest step can i continue from
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html

please help me i am stuck at this step


regards
amna khan
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Re: [gmx-users] about simulation runs

[amna khan]

and what about gromacs webserver ?
can i submit all my prepared files there ?


On Mon, Mar 4, 2013 at 10:27 PM, amna khan  wrote:

> 2230 atoms and same as tutorial
>
>
>
>
> On Mon, Mar 4, 2013 at 9:22 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 3/4/13 11:20 AM, amna khan wrote:
>>
>>> hi,
>>> i want to ask i have i3 laptop
>>> i want to run the 1ns simulations
>>> how much time it will take ?
>>>
>>>
>> There is no way to tell.  The time it takes depends on the size of the
>> system (number of atoms) and algorithms chosen.
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==**==
>> --
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Re: [gmx-users] about simulation runs

[amna khan]

2230 atoms and same as tutorial




On Mon, Mar 4, 2013 at 9:22 PM, Justin Lemkul  wrote:

>
>
> On 3/4/13 11:20 AM, amna khan wrote:
>
>> hi,
>> i want to ask i have i3 laptop
>> i want to run the 1ns simulations
>> how much time it will take ?
>>
>>
> There is no way to tell.  The time it takes depends on the size of the
> system (number of atoms) and algorithms chosen.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] rtp topology file for ligand

[amna khan]

i generated the ligand.gro by using the command

*editconf -g my_otp_ligand.pdb -o ligand.gro*
*
*
*WARNING: all CONECT records are ignored*
*Read 38 atoms*
*No velocities found*

it printed this and after this i did as mention in tutorial

it generated the bad box error  and the wc -l comand result is as follows

*and wc -l conf.gro
*
*2237 conf.gro*
*
*
*
*
*the first three lines *
*
2196
  705SER  N1  -3.373  -1.131   1.295
  705SER H12  -3.442  -1.166   1.232
  705SER H23  -3.339  -1.043   1.261
  705SER H34  -3.298  -1.196   1.303


and last three lines are
0_NFPHO   36  -0.376  -0.128   0.141
0_NFP   C26   37  -0.328   0.137  -0.081
0_NFP   C27   38  -0.293   0.373  -0.168
   9.21266   2.62220   3.05500


what is woring with ligand to gro converion ?

why this bad box error arose ?


regards
amna khan
*







On Tue, Feb 19, 2013 at 8:58 PM, Justin Lemkul  wrote:

>
>
> On 2/19/13 10:53 AM, amna khan wrote:
>
>> yes i am following this tutorial too
>>
>> this is my topology file for the ligand i made by atb
>>
>> *http://compbio.biosci.uq.edu.**au/atb/download.py?molid=7045<http://compbio.biosci.uq.edu.au/atb/download.py?molid=7045>
>>
>> *
>> *from here i got the .itp file and optimzed ligand.pdb file but what about
>>
>> the .gro file and .top file
>> *
>> *i ran that command to make the .gro and .top file of ligand 
>> *
>> *this is as follows
>> *
>>
>>
>> pdb2gmx -f my_ligand_opt.pdb -o my_ligand.gro -i my_ligand_posre.itp -p
>> my_ligand.top.
>>
>> this generated the fetal error
>>
>> Fatal error:
>> Residue 'LIG' not found in residue topology database
>>
>> SO WHAT SHOULD I DO ABOUT THIS PROBLEM
>>
>>
> Follow the tutorial more closely.  pdb2gmx will not deal with your ligand,
> so remove its coordinates from the protein-ligand complex and only run the
> protein through pdb2gmx.  You do not need pdb2gmx to make a topology for
> the ligand - you already have the topology in .itp format from ATB.  If you
> need the ligand coordinates in .gro format, simply transform from .pdb to
> .gro using edticonf. The job of pdb2gmx is to produce a topology, an output
> coordinate file is a side effect.
>
> You do not need a separate .top file for the ligand.  A .top file is a
> system topology, encompassing all elements of the system and thus there can
> only be one.  Other molecules (like your ligand) are #included in the
> system .top file using .itp format.
>
> -Justin
>
>
>> On Tue, Feb 19, 2013 at 5:58 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 2/19/13 4:23 AM, amna khan wrote:
>>>
>>>  hi all,
>>>>
>>>>i generated the .itp file for my ligand using ATB,
>>>> and i have generated the protein topology file by using the forcefield
>>>> 13
>>>>
>>>> my question is i need to generate the *ligand .top and .gro files*
>>>>
>>>>
>>>> and when i use the command
>>>>
>>>>
>>>> *pdb2gmx -f  lig.pdb -o igand.gro -i lig.itp -p iig.top
>>>>
>>>> *
>>>> *the error arises that
>>>>
>>>> Fatal error:
>>>> Residue 'LIG' not found in residue topology database
>>>>
>>>>
>>>> *
>>>> what should i do ?
>>>>
>>>> how to create the rtp file for my ligand ... i have read the tutorail
>>>> but
>>>> i
>>>> am not getting it what steps* exactly should i do please please help me
>>>> and
>>>>
>>>> guide me in making the .rtp file for my ligand
>>>> *
>>>>
>>>>
>>>>  Chapter 5 of the manual describes .rtp format, but you don't need it.
>>>  You
>>> already have a ligand topology from ATB, so why ask pdb2gmx to do it over
>>> again?  Remove the ligand from the coordinate file and deal with it
>>> separately.  I don't know which tutorial you're referring to, but you
>>> should at least try to follow the protocol I describe here:
>>>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/<http://vt.edu/Pages/Personal/justin/**>
>>> gmx-tutorials/complex/index.html<http://www.bevanlab.**
>>> biochem.vt.edu/Pages/Personal/**justin/gmx-tutorials/complex/**
>>> index.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>
>>> >
>>>
>>> -Justin
>>>
>>> --
&g

Re: [gmx-users] rtp topology file for ligand

[amna khan]

yes i am following this tutorial too

this is my topology file for the ligand i made by atb

*http://compbio.biosci.uq.edu.au/atb/download.py?molid=7045

*
*from here i got the .itp file and optimzed ligand.pdb file but what about
the .gro file and .top file
*
*i ran that command to make the .gro and .top file of ligand 
*
*this is as follows
*

pdb2gmx -f my_ligand_opt.pdb -o my_ligand.gro -i my_ligand_posre.itp -p
my_ligand.top.

this generated the fetal error

Fatal error:
Residue 'LIG' not found in residue topology database

SO WHAT SHOULD I DO ABOUT THIS PROBLEM


On Tue, Feb 19, 2013 at 5:58 PM, Justin Lemkul  wrote:

>
>
> On 2/19/13 4:23 AM, amna khan wrote:
>
>> hi all,
>>
>>   i generated the .itp file for my ligand using ATB,
>> and i have generated the protein topology file by using the forcefield 13
>>
>> my question is i need to generate the *ligand .top and .gro files*
>>
>>
>> and when i use the command
>>
>>
>> *pdb2gmx -f  lig.pdb -o igand.gro -i lig.itp -p iig.top
>>
>> *
>> *the error arises that
>>
>> Fatal error:
>> Residue 'LIG' not found in residue topology database
>>
>>
>> *
>> what should i do ?
>>
>> how to create the rtp file for my ligand ... i have read the tutorail but
>> i
>> am not getting it what steps* exactly should i do please please help me
>> and
>>
>> guide me in making the .rtp file for my ligand
>> *
>>
>>
> Chapter 5 of the manual describes .rtp format, but you don't need it.  You
> already have a ligand topology from ATB, so why ask pdb2gmx to do it over
> again?  Remove the ligand from the coordinate file and deal with it
> separately.  I don't know which tutorial you're referring to, but you
> should at least try to follow the protocol I describe here:
>
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
> gmx-tutorials/complex/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] bad box error

[amna khan]

yes i have following this tutorial , the only difference i made is that i
didn't change the charges for ligand file.

it seems it is necessary to do this ?
am i rite ?


On Wed, Jan 30, 2013 at 1:51 AM, Justin Lemkul  wrote:

>
>
> On 1/29/13 3:46 PM, amna khan wrote:
>
>> i am using the best conformation of protein ligand file obtained after
>> docking results
>>
>> i made the .gro file  by
>>   pdb2gmx -f pro.pdb -o proceed.gro -water spc -missing -ignh
>>
>> then the ligand codinates from ligand,gro was obtained from prodrug sever,
>>
>
> Beware the quality of PRODRG topologies - they are never sufficiently
> accurate without manual reparameterization.  Using the coordinates from
> PRODRG may or may not cause problems.  Make sure you don't allow PRODRG to
> run EM on the structure, or else the docked pose will be altered.
>
>
>  then i pasted ligand coordinates in this file
>> the first three lines are
>>
>> Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
>>   2059
>>705SER  N1  -3.373  -1.131   1.295
>>705SER H12  -3.442  -1.166   1.232
>>705SER H23  -3.339  -1.043   1.261
>>705SER H34  -3.298  -1.196   1.303
>>
>> last three lines are
>>  1LIG  OAR 33 0.425 -0.911   1.194
>>  1LIG  CAC 34   0.593  -1.073   1.167
>>  1LIG  CAT 35   0.500  -1.191   1.198
>> 9.21266   2.49507   2.95990
>>
>>
>>
>>
>> and the output for command is
>> wc -l proceed.gro
>> 2100 proceed.gro
>>
>>
> This shows your problem.  You didn't account for the fact that you pasted
> in a ligand by properly incrementing the atom count on the second line of
> the file. Thus, when editconf reaches atom 2059, it expects to find box
> vectors on the next line, but instead finds another atom and gives you the
> "bad box" message. Your file actually has 2097 atoms (2100 - 3).
>
> Note that there is a protein-ligand tutorial available if these concepts
> are unfamiliar to you.
>
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
> gmx-tutorials/complex/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html>
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
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Re: [gmx-users] bad box error

[amna khan]

i am using the best conformation of protein ligand file obtained after
docking results

i made the .gro file  by
 pdb2gmx -f pro.pdb -o proceed.gro -water spc -missing -ignh

then the ligand codinates from ligand,gro was obtained from prodrug sever,
then i pasted ligand coordinates in this file
the first three lines are

Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
 2059
  705SER  N1  -3.373  -1.131   1.295
  705SER H12  -3.442  -1.166   1.232
  705SER H23  -3.339  -1.043   1.261
  705SER H34  -3.298  -1.196   1.303

last three lines are
1LIG  OAR 33   0.425  -0.911   1.194
1LIG  CAC 34   0.593  -1.073   1.167
1LIG  CAT 35   0.500  -1.191   1.198
   9.21266   2.49507   2.95990




and the output for command is
wc -l proceed.gro
2100 proceed.gro



On Wed, Jan 30, 2013 at 1:20 AM, Justin Lemkul  wrote:

>
>
> On 1/29/13 3:07 PM, amna khan wrote:
>
>> so, i could i correct this ?
>>
>>
> Probably, but we need a lot more information if you want help:
>
> 1. Describe what your system is and how you constructed conf.gro
> 2. Post the first 3 and last 3 lines of conf.gro
> 3. Post the output of wc -l conf.gro
>
> -Justin
>
>
>>
>> On Wed, Jan 30, 2013 at 12:52 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 1/29/13 2:43 PM, az kalsom wrote:
>>>
>>>  hi ,
>>>>
>>>> when i use "editconf" to generate a dodecahedron box with the command
>>>>
>>>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>>>>
>>>> the output shows the warning
>>>>
>>>> bad box in file
>>>>
>>>> generated  a new cubic box  9.213 x2.495 x2.960
>>>>
>>>>
>>>> what is the mean of "bad box in file"?
>>>>and why editconf generates a cubic box?
>>>>
>>>>
>>>>  Whatever input you have provided is malformatted.
>>>
>>> -Justin
>>>
>>> --
>>> ====
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ====
>>>
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
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>>> posting!
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>>> >
>>>
>>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
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Re: [gmx-users] bad box error

[amna khan]

so, i could i correct this ?



On Wed, Jan 30, 2013 at 12:52 AM, Justin Lemkul  wrote:

>
>
> On 1/29/13 2:43 PM, az kalsom wrote:
>
>> hi ,
>>
>> when i use "editconf" to generate a dodecahedron box with the command
>>
>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>>
>> the output shows the warning
>>
>> bad box in file
>>
>> generated  a new cubic box  9.213 x2.495 x2.960
>>
>>
>> what is the mean of "bad box in file"?
>>   and why editconf generates a cubic box?
>>
>>
> Whatever input you have provided is malformatted.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
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Re: [gmx-users] dna-drug simulations

[amna khan]

hi,
i want to simulate the DNA with gormacs forcefield, accrding to literatre
 Charm and amber are best to be used but
GROMACS96 43A1 force field can be also used

the error with GROMACS96 43A1 is
*Fatal error:*
*Residue 'DA' not found in residue topology database*

this is  same error with gromacs 43a2. gromacs 45 3a, gromacs 53a5, gromacs
53 a6 and opls/a
[DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
 [DEPRECATED] Gromacs force field (see manual)   [DEPRECATED] Gromacs force
field with hydrogens for N



with charm force field is
*Fatal error:*
*Atom H7 in residue DA 1 was not found in rtp entry DA with 30 atoms*
*while sorting atoms.*
*
*
i have also use -ignh option, but stiill the problem comes which is as
follows
*Fatal error:*
*Atom ''H5 in residue DA 1 was not found in rtp entry DA with 30 atoms*
*while sorting ato*ms.


for amber
*Fatal error:*
*Atom H7 in residue DA 1 was not found in rtp entry DA5 with 30 atoms*
*while sorting atoms.*


*and by -ignh command *
*
*
*
Fatal error:
Atom ''H5 in residue DA 1 was not found in rtp entry DA5 with 30 atoms
while sorting atoms.


the error with charm and amber forcefiled are same

*
how to reomve this error for groamcs 43a1 or amber or chrm forcefield



On Sat, Jan 26, 2013 at 6:13 PM, Justin Lemkul  wrote:

>
>
> On 1/26/13 4:18 AM, amna khan wrote:
>
>> hi, all ,
>>
>> i want to simulate dna with ligand/drug
>>
>> i am getting error in generating he topology for dna .
>>
>
> We can't help you unless you show us what the error is and provide (at the
> very least) your exact pdb2gmx command.
>
>
>  I'm unable to do using the  pdb2gmx with any of the force fields. Could
>> anyone please tell if I can get any tutorial for the DNA-drug simulation.
>>
>
> Exercise Google here.  If it exists, you should be able to find it by
> searching or visiting gromacs.org.
>
>
>  or which forcefield should i use ?
>>
>>
> What does your analysis of the literature suggest would be the best choice?
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] gromacs demo

[amna khan]

the command
/usr/share/gromacs/tutor/gmxdemo/demo

no such cooamnd found...

cd  /usr/share/gromacs/tutor/gmxdemo/demo

permsion denied

sudo /usr/share/gromacs/tutor/gmxdemo/demo

comand not found

i am not getting any results




On Thu, Jan 3, 2013 at 4:19 PM, Justin Lemkul  wrote:

>
>
> On 1/3/13 6:06 AM, amna khan wrote:
>
>> hi all.
>>
>> i am a beginer user of ubuntu and gromacs
>> i installed gormacs on ubuntu 12.10 and now want to run demo , i dont know
>> how to run this correctly
>>
>> i do by typing cd /usr/share/gromacs/tutor/**gmxdemo
>>
>> it gives nothing as output
>>
>>
> You changed into a directory; you didn't actually run anything.  There's a
> script called 'demo' in that directory that you need to execute to get it
> to run.
>
>
>
>> help me please in running the demo
>>
>>
> The demo is significantly less useful than the many tutorials provided
> online.
>
> http://www.gromacs.org/**Documentation/Tutorials<http://www.gromacs.org/Documentation/Tutorials>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
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>  posting!
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