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

[Justin Lemkul]

On 4/1/16 4:31 AM, bio hpc wrote:

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



The specifics depend on the input file itself, and different programs write 
different names (an unfortunate truth that not everyone sticks to IUPAC/IUPAB 
nomenclature), and sometimes force fields have their own quirks.  It's just a 
listing of sed commands based on each residue.  But the easiest way has already 
been suggested: use -ignh and specify protonation states when running pdb2gmx. 
The initial H coordinates themselves are going to change as soon as you run 
energy minimization, so preserving these exact coordinates has no bearing on 
anything of importance.  Key interactions will be preserved only if the force 
field represents them correctly, which is another issue entirely.


-Justin


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



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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] 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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>>> 
>>> 
>>> 
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
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>>> Gromacs Users mailing list
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>>> * Please search the archive at 
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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] Use pdb file generated with Maestro, in Gromacs

[Justin Lemkul]

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



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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] 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!
 
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 * 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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>>> 
>>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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>> --
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>> posting!
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>> 
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> -- 
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Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

[Tsjerk Wassenaar]

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

[sun]

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
>> 
>> * 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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> 
> * Please search the archive at 
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Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

[rajendra kumar]

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

[SAKO MIRZAIE]

Hi,
use -ignh flag in pdb2gmx, or you can use of "swiss pdbviewer"
software to correct your pdb.

On 3/30/16, 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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-- 
***
sako mirzaie
PhD in biochemistry, science faculty, Islamic azad university of
sanandaj, sanandaj, Iran
http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie

http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie

http://scholar.google.com/citations?user=viwZvVAJ=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
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