Re: [gmx-users] ignoring -h atoms

[Erik Marklund]

Dear Maria,

I’m not saying that it never makes a difference for the topology generation, 
but it depends on the quality of your input structure. Justin and I both gave 
examples of why you might want to use it. When you do, -ignh ignores the 
hydrogens in the input pdb and uses the rtp to model new ones. I don’t 
understand why you say that the “ff its ignore it”.

As for what is most reliable, that again depends on the quality of the input 
structure. Pdb2gmx -ignh normally does a good job.

Kind regards,
Erik

> On 8 Feb 2017, at 07:20, maria khan  wrote:
> 
> Dear ERIK..
> 
> """..No. -ignh ignores the hydrogen atoms in the input structure, but uses
> the rtp file(s) to generate new hydrogens. This is useful, for example,
> when some hydrogens are missing in the pdb file. The structure and topology
> will therefore contain hydrogens in the end also with -ignh."""..
> 
> 
> now i have confusion if the ff ist ignore it and then in rtp files consider
> it..so why it at ist it ignores..there is no need to do so.after all h-atom
> will be same if it is in input file or when later form by rtp file.
> 
> secondly what will be the consequences,,if in case it is ignored or not
> ignored..would it make difference to results in both cases.and if there
> would difference in results,,what kind of results are more reliable.???
> 
> regards..
> -- 
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[gmx-users] ignoring -h atoms

[maria khan]

Dear ERIK..

"""..No. -ignh ignores the hydrogen atoms in the input structure, but uses
the rtp file(s) to generate new hydrogens. This is useful, for example,
when some hydrogens are missing in the pdb file. The structure and topology
will therefore contain hydrogens in the end also with -ignh."""..


now i have confusion if the ff ist ignore it and then in rtp files consider
it..so why it at ist it ignores..there is no need to do so.after all h-atom
will be same if it is in input file or when later form by rtp file.

secondly what will be the consequences,,if in case it is ignored or not
ignored..would it make difference to results in both cases.and if there
would difference in results,,what kind of results are more reliable.???

regards..
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Re: [gmx-users] Ignoring H-atoms.

[Justin Lemkul]

On 2/7/17 3:42 AM, Amir Zeb wrote:

Thanks Erik,

I got the explanation you kindly posted regarding the posted discussion.

I would like to extend the question that if some one does not flag the
-ignh, so does it mean that the input H-atoms are still there and the force
field will consider them during the rtp file generation?
Further more, if the case is likely not to flag the -ignh, what might be
the possible consequences?



The -ignh flag has one purpose, as Erik said, which is to ignore H atoms in the 
input coordinate file.  It does not necessarily have any relationship to any 
force field.  All force fields have their own conventions as to whether or not H 
atoms are represented (united-atom vs. all-atom, for instance) and how they're 
named (although this much is usually consistent).


The -ignh flag does one thing to potentially serve two purposes:

1. Avoid nomenclature inconsistencies.  Unfortunately, many programs use their 
own conventions for naming H atoms, which are often inconsistent with standard 
nomenclature.  Using -ignh gets rid of most problems instead of the user having 
to do find-and-replace throughout their file.


2. United-atom force fields.  An experimental or modeled structure with H will 
not be appropriate if you're using a UA force field (e.g. GROMOS), so ignoring 
the H will overcome errors that would arise about H atoms being found in the 
coordinate file that are not expected/needed.


-Justin

--
==

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] Ignoring H-atoms.

[Amir Zeb]

Thanks Erik,

I got the explanation you kindly posted regarding the posted discussion.

I would like to extend the question that if some one does not flag the
-ignh, so does it mean that the input H-atoms are still there and the force
field will consider them during the rtp file generation?
Further more, if the case is likely not to flag the -ignh, what might be
the possible consequences?

I trust to listen to your precious negotiation.

Cheers!

Amir

On Tue, Feb 7, 2017 at 12:21 AM, Erik Marklund 
wrote:

>
>
> > On 7 Feb 2017, at 08:35, Amir Zeb  wrote:
> >
> > Hello Maria,
> >
> > f igoring h-atom command is applied ,,then forcefield will ignore all the
> > added h-atoms
> >
> > What I know about -ignh flag, it does not mean to remove the h-atoms,
> > alternatively means that during the topology generation, the force field
> is
> > considering the h-atoms as the light atoms and does not pay much
> attention
> > to consider their parameters so accurately.
>
> No. -ignh ignores the hydrogen atoms in the input structure, but uses the
> rtp file(s) to generate new hydrogens. This is useful, for example, when
> some hydrogens are missing in the pdb file. The structure and topology will
> therefore contain hydrogens in the end also with -ignh.
>
> Kind regards,
> Erik
>
> >
> > it would be a vaccum simulation if
> > the h-atom will be ignored
> >
> > Also, in case of vacuum simulation, I think there is no water addition,
> > while here we are gonna adding the water during the salvation step  of
> the
> > procedure. So, I think you don't need to worry about it.
> >
> > At the end, I would like to appraise in deep the explanation of other
> users.
> >
> > Cheers!
> >
> > Amir
> >
> > On Mon, Feb 6, 2017 at 10:12 PM, maria khan 
> > wrote:
> >
> >> Dear Gromacs users,,
> >>
> >> if igoring h-atom command is applied ,,then forcefield will ignore all
> the
> >> added h-atoms,,,so my question is then it would be a vaccum simulation
> if
> >> the h-atom will be ignored,,secondly the results will be also differnt
> then
> >> when h-atoms are considered.
> >>
> >> Regards..
> >> --
> >> Gromacs Users mailing list
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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
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Re: [gmx-users] Ignoring H-atoms.

[Erik Marklund]

> On 7 Feb 2017, at 08:35, Amir Zeb  wrote:
> 
> Hello Maria,
> 
> f igoring h-atom command is applied ,,then forcefield will ignore all the
> added h-atoms
> 
> What I know about -ignh flag, it does not mean to remove the h-atoms,
> alternatively means that during the topology generation, the force field is
> considering the h-atoms as the light atoms and does not pay much attention
> to consider their parameters so accurately.

No. -ignh ignores the hydrogen atoms in the input structure, but uses the rtp 
file(s) to generate new hydrogens. This is useful, for example, when some 
hydrogens are missing in the pdb file. The structure and topology will 
therefore contain hydrogens in the end also with -ignh.

Kind regards,
Erik

> 
> it would be a vaccum simulation if
> the h-atom will be ignored
> 
> Also, in case of vacuum simulation, I think there is no water addition,
> while here we are gonna adding the water during the salvation step  of the
> procedure. So, I think you don't need to worry about it.
> 
> At the end, I would like to appraise in deep the explanation of other users.
> 
> Cheers!
> 
> Amir
> 
> On Mon, Feb 6, 2017 at 10:12 PM, maria khan 
> wrote:
> 
>> Dear Gromacs users,,
>> 
>> if igoring h-atom command is applied ,,then forcefield will ignore all the
>> added h-atoms,,,so my question is then it would be a vaccum simulation if
>> the h-atom will be ignored,,secondly the results will be also differnt then
>> when h-atoms are considered.
>> 
>> Regards..
>> --
>> 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] Ignoring H-atoms.

[Amir Zeb]

Hello Maria,

f igoring h-atom command is applied ,,then forcefield will ignore all the
added h-atoms

What I know about -ignh flag, it does not mean to remove the h-atoms,
alternatively means that during the topology generation, the force field is
considering the h-atoms as the light atoms and does not pay much attention
to consider their parameters so accurately.

it would be a vaccum simulation if
the h-atom will be ignored

Also, in case of vacuum simulation, I think there is no water addition,
while here we are gonna adding the water during the salvation step  of the
procedure. So, I think you don't need to worry about it.

At the end, I would like to appraise in deep the explanation of other users.

Cheers!

Amir

On Mon, Feb 6, 2017 at 10:12 PM, maria khan 
wrote:

> Dear Gromacs users,,
>
> if igoring h-atom command is applied ,,then forcefield will ignore all the
> added h-atoms,,,so my question is then it would be a vaccum simulation if
> the h-atom will be ignored,,secondly the results will be also differnt then
> when h-atoms are considered.
>
> Regards..
> --
> 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.
>
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[gmx-users] Ignoring H-atoms.

[maria khan]

Dear Gromacs users,,

if igoring h-atom command is applied ,,then forcefield will ignore all the
added h-atoms,,,so my question is then it would be a vaccum simulation if
the h-atom will be ignored,,secondly the results will be also differnt then
when h-atoms are considered.

Regards..
-- 
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