Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

[bio hpc]

Did anybody of you wrote such script or can that be found in some repository?

> El 31/3/2016, a las 13:04, Justin Lemkul  escribió:
> 
> 
> 
> On 3/31/16 6:55 AM, bio hpc wrote:
>> Thanks.
>> Apart from this, is is there some script that keeps my original hydrogens 
>> from Maestro?
>> 
> 
> Rename with sed according to what the force field expects.
> 
> -Justin
> 
>>> El 30/3/2016, a las 19:43, Tsjerk Wassenaar  escribió:
>>> 
>>> Hey :)
>>> 
>>> -ignh does ignore the hydrogens in the input file. It builds those
>>> hydrogens that are specified in the force field. For histidines, the
>>> protonation state is determined from the possible hydrogen-bonded network,
>>> but it is possible to assign specific states interactively, using the
>>> option -his, or by specifying the residue name in the input file.
>>> 
>>> Hope it helps,
>>> 
>>> Tsjerk
>>> 
>>> On Wed, Mar 30, 2016 at 4:42 PM, sun  wrote:
>>> 
>>>> I think using -ignh does not "remove" hydrogens. Hence, you can use it.
>>>> 
>>>> Sent from my iPhone
>>>> 
>>>>> On 30-Mar-2016, at 6:04 pm, rajendra kumar  wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> As suggested above, use -ignh to ignore hydrogen atoms. To use a specific
>>>>> Histidine, you may change residue name HIS to
>>>> HIP(Amber)/HSP(Charmm)/HISH(
>>>>> ​OPLS​
>>>>> ) or HID(Amber)/HSD(Charmm)/HISD(
>>>>> ​OPLS​
>>>>> ) or HIE(Amber)/HSE(Charmm)/HISE(
>>>>> ​OPLS​
>>>>> ) either in PDB file or interactively through pdb2gmx usng -his command.
>>>>> 
>>>>> 
>>>>>> On Wed, Mar 30, 2016 at 12:27 PM, bio hpc  wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> we have created some protein pdb files with Maestro. When we try to un
>>>> an
>>>>>> MD simulation with gromacs, we get errors like:
>>>>>> 
>>>>>>>> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14
>>>> atoms
>>>>>> 
>>>>>> I tried to find a solution and it seems that internal gromacs dictionary
>>>>>> for hydrogens is different from the one from Maestro and other formats.
>>>> It
>>>>>> seems, from what I read, that one must convert all hydrogen types to
>>>>>> Gromacs format. Is is there any script that can do this automatically?
>>>>>> 
>>>>>> Of course, there is the option “ignore hydrogens”, but this would be bad
>>>>>> for us, since we need some histidines in the binding site, and so on.
>>>>>> 
>>>>>> Thanks,
>>>>>> BIO-HPC
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>> 
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
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>>>>>> send a mail to gmx-users-requ...@gromacs.org.
>>>>> --
>>>>> Gromacs Users mailing list
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Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

[bio hpc]

My problem is not excel or whatever graphical program. I just need the data, in 
an automatic way. Then I can use either matplotlib or similar to get the plots 
automatically. But my question is if there is somewhere a repository of gromacs 
scripts with a script doing an analysis of the protein-ligand itneractions 
during trajectory. I do not think to be the only one requesting this


> El 30/3/2016, a las 6:46, Sun Iba  escribió:
> 
> i am sorry, i replied prior to looking at your figure. Actually, i have
> never came across plotting data in this matter. However, I believe you have
> tabulated data, so you can use Origin or excel for generating similar
> images. You need little effort to arrange the data in desired manner.
> Best Wishes
> 
> On Wed, Mar 30, 2016 at 3:15 AM, bio hpc  wrote:
> 
>> Hi,
>> 
>> after a protein-ligand simulation with gromacs, I would like to be able to
>> generate a diagram/figure with information about protein-ligand
>> interactions, something like this:
>> 
>> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg <
>> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg>
>> 
>> I had a look to all gromacs tools but found nothing similar to this. Where
>> can I start from?
>> 
>> Thanks,
>> 
>> biohpc
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
> -- 
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Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

[bio hpc]

Thanks. 
Apart from this, is is there some script that keeps my original hydrogens from 
Maestro?

> El 30/3/2016, a las 19:43, Tsjerk Wassenaar  escribió:
> 
> Hey :)
> 
> -ignh does ignore the hydrogens in the input file. It builds those
> hydrogens that are specified in the force field. For histidines, the
> protonation state is determined from the possible hydrogen-bonded network,
> but it is possible to assign specific states interactively, using the
> option -his, or by specifying the residue name in the input file.
> 
> Hope it helps,
> 
> Tsjerk
> 
> On Wed, Mar 30, 2016 at 4:42 PM, sun  wrote:
> 
>> I think using -ignh does not "remove" hydrogens. Hence, you can use it.
>> 
>> Sent from my iPhone
>> 
>>> On 30-Mar-2016, at 6:04 pm, rajendra kumar  wrote:
>>> 
>>> Hi,
>>> 
>>> As suggested above, use -ignh to ignore hydrogen atoms. To use a specific
>>> Histidine, you may change residue name HIS to
>> HIP(Amber)/HSP(Charmm)/HISH(
>>> ​OPLS​
>>> ) or HID(Amber)/HSD(Charmm)/HISD(
>>> ​OPLS​
>>> ) or HIE(Amber)/HSE(Charmm)/HISE(
>>> ​OPLS​
>>> ) either in PDB file or interactively through pdb2gmx usng -his command.
>>> 
>>> 
>>>> On Wed, Mar 30, 2016 at 12:27 PM, bio hpc  wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> we have created some protein pdb files with Maestro. When we try to un
>> an
>>>> MD simulation with gromacs, we get errors like:
>>>> 
>>>>>> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14
>> atoms
>>>> 
>>>> I tried to find a solution and it seems that internal gromacs dictionary
>>>> for hydrogens is different from the one from Maestro and other formats.
>> It
>>>> seems, from what I read, that one must convert all hydrogen types to
>>>> Gromacs format. Is is there any script that can do this automatically?
>>>> 
>>>> Of course, there is the option “ignore hydrogens”, but this would be bad
>>>> for us, since we need some histidines in the binding site, and so on.
>>>> 
>>>> Thanks,
>>>> BIO-HPC
>>>> 
>>>> 
>>>> 
>>>> --
>>>> 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
>>> 
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>> --
>> Gromacs Users mailing list
>> 
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>> 
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> -- 
> Gromacs Users mailing list
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[gmx-users] Use pdb file generated with Maestro, in Gromacs

[bio hpc]

Hi,

we have created some protein pdb files with Maestro. When we try to un an MD 
simulation with gromacs, we get errors like:

>> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14 atoms

I tried to find a solution and it seems that internal gromacs dictionary for 
hydrogens is different from the one from Maestro and other formats. It seems, 
from what I read, that one must convert all hydrogen types to Gromacs format. 
Is is there any script that can do this automatically?

Of course, there is the option “ignore hydrogens”, but this would be bad for 
us, since we need some histidines in the binding site, and so on.

Thanks,
BIO-HPC



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[gmx-users] Generate diagram/figure with information about protein-ligand interactions

[bio hpc]

Hi,

after a protein-ligand simulation with gromacs, I would like to be able to 
generate a diagram/figure with information about protein-ligand interactions, 
something like this:

https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg 


I had a look to all gromacs tools but found nothing similar to this. Where can 
I start from?

Thanks,

biohpc

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