Re: [gmx-users] gromacs ligand topology file for "GNP"

2017-09-07 Thread Justin Lemkul 



On 9/7/17 9:23 AM, Deep kumar wrote:

Hello,

On Thu, Sep 7, 2017 at 1:11 AM, Justin Lemkul  wrote:



On 9/6/17 3:46 PM, Deep kumar wrote:


Dear All,

I have produced the "ITP" files of the ligands using ATB server.  I am
mentioning the steps here, please let me know if you think anything is
wrong.

a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.

b) Entered the "net charge" by calculating like this using chimera: (added
Hydrogen prior to calculating net charge and produced .mol2 file to
calculate the net charge)

from chimera import openModels, Molecule
from AddCharge import estimateNetCharge
from OpenSave import osOpen
output = osOpen("charge-estimates", "w")
for m in openModels.list(modelTypes=[Molecule]):
  print>>output, m, m.name, estimateNetCharge(m.atoms)
output.close()

the "net charge" of "RND" was shown to be "2".



Does that make sense?  What is RND?


RND is the ligand found in 4NYM.pdb file. I am trying to make a system of
this pdb for MD.



I understand that; I'm trying to get you to think a little bit about the 
chemistry.  What are the titratable groups and what are their pKa 
values?  Does a +2 net charge make sense?  This would be pretty uncommon 
for any small molecule that is considered an inhibitor/ligand for a protein.




c) submitted the entry and after completion, downloaded the file as below:

  From "Molecular Dynamics(MD) files", chose "Forcefield" to be
"Gromos54A7"
& "Format" to be "Gromacs", and downloaded "All Atom" ITP file.

I am running the MD on Gromacs version 5.1. I have prepared the protein
topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.

Please let me know if I did right or if anything else is needed to be
done.

Secondly, I also need .gro file of the ligand. Can you please let me know
how can I get that. The tutorial am following (
http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I
have to prepare a position restraint file "posre_RND.itp" from the
"RND.gro" file, so how can I get the "RND.gro" file?



You don't need a .gro file to generate a position restraint file; as with
most operations in GROMACS, you can use any coordinate file format here.
If you *really* want to use .gro, you can transform between formats with
editconf.

And lastly, please let me know how to generate topology of "GNP" molecule

with gromos53A6 FF. I tried ATB but it says error "
Error recorded: Unsupported bond length encountered: 0.56nm (PA-O5'). This
often indicates there is an error in the submitted structure.
"



The error here is pretty clear.  You have a bad geometry for this molecule
with a bond length that is about 3 times longer than it really should be.
Visualizing the coordinates should make this apparent since ATB is telling
you exactly which bond is problematic.


Thanks, can you please let me know how can I solve this problem?


Look at the geometry - is there a problem?  Has the PDB file you're 
supplying for GNP been modified in any way?  Does it visualize 
properly?  I doubt an experimental assignment of a 0.56-nm bond would be 
made when it should be on the order of 0.16 nm or so.


-Justin




-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] gromacs ligand topology file for "GNP"

2017-09-07 Thread Deep kumar 
Hello,

On Thu, Sep 7, 2017 at 1:11 AM, Justin Lemkul  wrote:

>
>
> On 9/6/17 3:46 PM, Deep kumar wrote:
>
>> Dear All,
>>
>> I have produced the "ITP" files of the ligands using ATB server.  I am
>> mentioning the steps here, please let me know if you think anything is
>> wrong.
>>
>> a) uploaded the coordinates of ligand "RND" on ATB server. I chose
>> "heteromoelcule" molecule type.
>>
>> b) Entered the "net charge" by calculating like this using chimera: (added
>> Hydrogen prior to calculating net charge and produced .mol2 file to
>> calculate the net charge)
>>
>> from chimera import openModels, Molecule
>> from AddCharge import estimateNetCharge
>> from OpenSave import osOpen
>> output = osOpen("charge-estimates", "w")
>> for m in openModels.list(modelTypes=[Molecule]):
>>  print>>output, m, m.name, estimateNetCharge(m.atoms)
>> output.close()
>>
>> the "net charge" of "RND" was shown to be "2".
>>
>>
> Does that make sense?  What is RND?


RND is the ligand found in 4NYM.pdb file. I am trying to make a system of
this pdb for MD.


>
>
> c) submitted the entry and after completion, downloaded the file as below:
>>
>>  From "Molecular Dynamics(MD) files", chose "Forcefield" to be
>> "Gromos54A7"
>> & "Format" to be "Gromacs", and downloaded "All Atom" ITP file.
>>
>> I am running the MD on Gromacs version 5.1. I have prepared the protein
>> topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.
>>
>> Please let me know if I did right or if anything else is needed to be
>> done.
>>
>> Secondly, I also need .gro file of the ligand. Can you please let me know
>> how can I get that. The tutorial am following (
>> http://www.bevanlab.biochem.
>> vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I
>> have to prepare a position restraint file "posre_RND.itp" from the
>> "RND.gro" file, so how can I get the "RND.gro" file?
>>
>>
> You don't need a .gro file to generate a position restraint file; as with
> most operations in GROMACS, you can use any coordinate file format here.
> If you *really* want to use .gro, you can transform between formats with
> editconf.
>
> And lastly, please let me know how to generate topology of "GNP" molecule
>> with gromos53A6 FF. I tried ATB but it says error "
>> Error recorded: Unsupported bond length encountered: 0.56nm (PA-O5'). This
>> often indicates there is an error in the submitted structure.
>> "
>>
>>
> The error here is pretty clear.  You have a bad geometry for this molecule
> with a bond length that is about 3 times longer than it really should be.
> Visualizing the coordinates should make this apparent since ATB is telling
> you exactly which bond is problematic.
>

Thanks, can you please let me know how can I solve this problem?


>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
> --
> 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] gromacs ligand topology file for "GNP"

2017-09-06 Thread Justin Lemkul 



On 9/6/17 3:46 PM, Deep kumar wrote:

Dear All,

I have produced the "ITP" files of the ligands using ATB server.  I am
mentioning the steps here, please let me know if you think anything is
wrong.

a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.

b) Entered the "net charge" by calculating like this using chimera: (added
Hydrogen prior to calculating net charge and produced .mol2 file to
calculate the net charge)

from chimera import openModels, Molecule
from AddCharge import estimateNetCharge
from OpenSave import osOpen
output = osOpen("charge-estimates", "w")
for m in openModels.list(modelTypes=[Molecule]):
 print>>output, m, m.name, estimateNetCharge(m.atoms)
output.close()

the "net charge" of "RND" was shown to be "2".



Does that make sense?  What is RND?


c) submitted the entry and after completion, downloaded the file as below:

 From "Molecular Dynamics(MD) files", chose "Forcefield" to be "Gromos54A7"
& "Format" to be "Gromacs", and downloaded "All Atom" ITP file.

I am running the MD on Gromacs version 5.1. I have prepared the protein
topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.

Please let me know if I did right or if anything else is needed to be done.

Secondly, I also need .gro file of the ligand. Can you please let me know
how can I get that. The tutorial am following (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I
have to prepare a position restraint file "posre_RND.itp" from the
"RND.gro" file, so how can I get the "RND.gro" file?



You don't need a .gro file to generate a position restraint file; as with most 
operations in GROMACS, you can use any coordinate file format here.  If you 
*really* want to use .gro, you can transform between formats with editconf.



And lastly, please let me know how to generate topology of "GNP" molecule
with gromos53A6 FF. I tried ATB but it says error "
Error recorded: Unsupported bond length encountered: 0.56nm (PA-O5'). This
often indicates there is an error in the submitted structure.
"



The error here is pretty clear.  You have a bad geometry for this molecule with 
a bond length that is about 3 times longer than it really should be. 
Visualizing the coordinates should make this apparent since ATB is telling you 
exactly which bond is problematic.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
--
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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mail to gmx-users-requ...@gromacs.org.

[gmx-users] gromacs ligand topology file for "GNP"

2017-09-06 Thread Deep kumar 
Dear All,

I have produced the "ITP" files of the ligands using ATB server.  I am
mentioning the steps here, please let me know if you think anything is
wrong.

a) uploaded the coordinates of ligand "RND" on ATB server. I chose
"heteromoelcule" molecule type.

b) Entered the "net charge" by calculating like this using chimera: (added
Hydrogen prior to calculating net charge and produced .mol2 file to
calculate the net charge)

from chimera import openModels, Molecule
from AddCharge import estimateNetCharge
from OpenSave import osOpen
output = osOpen("charge-estimates", "w")
for m in openModels.list(modelTypes=[Molecule]):
print>>output, m, m.name, estimateNetCharge(m.atoms)
output.close()

the "net charge" of "RND" was shown to be "2".

c) submitted the entry and after completion, downloaded the file as below:

>From "Molecular Dynamics(MD) files", chose "Forcefield" to be "Gromos54A7"
& "Format" to be "Gromacs", and downloaded "All Atom" ITP file.

I am running the MD on Gromacs version 5.1. I have prepared the protein
topology using "pdb2gmx" of Gromacs using "Gromos96 54A7" force field.

Please let me know if I did right or if anything else is needed to be done.

Secondly, I also need .gro file of the ligand. Can you please let me know
how can I get that. The tutorial am following (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html) says, I
have to prepare a position restraint file "posre_RND.itp" from the
"RND.gro" file, so how can I get the "RND.gro" file?

And lastly, please let me know how to generate topology of "GNP" molecule
with gromos53A6 FF. I tried ATB but it says error "
Error recorded: Unsupported bond length encountered: 0.56nm (PA-O5'). This
often indicates there is an error in the submitted structure.
"

Thanks,
Deep
-- 
Gromacs Users mailing list

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