Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-15 Thread Justin Lemkul 



On 3/14/18 11:57 PM, Dilip H N wrote:

1) I tried with the Nitrogen atom of glycine and the oxygen atom of water
also using the command

gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -num abc.xvg

but still, i am getting the same error as:-
Specify 2 groups to analyze:
Group 0 (  N) has 1 elements
Group 1 ( OW) has   511 elements
Select a group: 0
Selected 0: 'N'
Select a group: 1
Selected 1: 'OW'
Checking for overlap in atoms between N and OW
Calculating hydrogen bonds between N (1 atoms) and OW (511 atoms)
Found 0 donors and 512 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

2) I tried to find out the distance between Calpha(Ca) and Ow from the
command
gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -dist abc.xvg

but still, i am getting the same error as above one.

Any suggestions...


Neither of your groups has any H atoms. gmx hbond can't calculate 
hydrogen bonds without them.


-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.

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-14 Thread Joe Jordan 
The problem you are running into is that the tool you are using is not
designed to be used in this way. As a suggestion for alternatives, you
could use gmx pairdist to find all N and OW atomtypes within some distance
of each other and then run that through gmx angle. You could also consider
e.g. using MDAnalysis where it is pretty easy to redefine the h-bond donors
and acceptors.

On Thu, Mar 15, 2018 at 4:57 AM, Dilip H N 
wrote:

> 1) I tried with the Nitrogen atom of glycine and the oxygen atom of water
> also using the command
>
> gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -num abc.xvg
>
> but still, i am getting the same error as:-
> Specify 2 groups to analyze:
> Group 0 (  N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 0
> Selected 0: 'N'
> Select a group: 1
> Selected 1: 'OW'
> Checking for overlap in atoms between N and OW
> Calculating hydrogen bonds between N (1 atoms) and OW (511 atoms)
> Found 0 donors and 512 acceptors
> No Donors found
> ---
> Program: gmx hbond, version 2016.2
> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
> Fatal error:
> Nothing to be done
>
> 2) I tried to find out the distance between Calpha(Ca) and Ow from the
> command
> gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -dist abc.xvg
>
> but still, i am getting the same error as above one.
>
> Any suggestions...
>
> Thank you.
>
> ‌
>  Sent with Mailtrack
>  signaturevirality&>
>
> On Tue, Mar 13, 2018 at 7:34 PM, Erik Marklund 
> wrote:
>
> > A shortcut would be to only look at the C-O distance, which can be done
> > with gmx hbond without modification.
> >
> > Kind regards,
> > Erik
> >
> > > On 13 Mar 2018, at 15:01, Jeremy T First 
> > wrote:
> > >
> > > Hi Dilip,
> > >
> > > There is quite a bit of literature, especially recently, that considers
> > the
> > > alpha carbon as a hydrogen bond donor. How well this is represented in
> > your
> > > simulation will depend on your force field.
> > >
> > > You will likely need to develop your own gromacs tool to calculate
> this,
> > > but it should be quite easy. We recently wrote a tool that does
> something
> > > very similar, but you would need to edit it for your own purposes. If
> you
> > > are interested in using our code as a template, feel free to contact me
> > off
> > > list.
> > >
> > > Good luck!
> > > Jeremy
> > >
> > >
> > >
> > >
> > > Jeremy Todd First
> > > Webb Research Group
> > > University of Texas at Austin
> > > jeremy_fi...@utexas.edu
> > > (443) 243-1187
> > >
> > > On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund <
> erik.markl...@kemi.uu.se
> > >
> > > wrote:
> > >
> > >> The point is that Calpha don’t form hydrogen bonds.
> > >>
> > >> Erik
> > >> __
> > >> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> > >> Department of Chemistry – BMC, Uppsala University
> > >> +46 (0)18 471 4539
> > >> erik.markl...@kemi.uu.se
> > >>
> > >> On 13 Mar 2018, at 13:20, Dilip H N  mailto:
> > >> cy16f01.di...@nitk.edu.in>> wrote:
> > >>
> > >> Then how can i calculate the hydrogen bonding between C-alpha and
> Oxygen
> > >> atom of water molecules..??
> > >> What are the other possible ways..??
> > >>
> > >>
> > >>
> > >>  Sent with Mailtrack
> > >>  > signature&utm_campaign=
> > >> signaturevirality& > >> gmail&utm_medium=signature&utm_campaign=signaturevirality&>>
> > >>
> > >> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund <
> > erik.markl...@kemi.uu.se<
> > >> mailto:erik.markl...@kemi.uu.se>>
> > >> wrote:
> > >>
> > >> Dear Dilip,
> > >>
> > >> The Calpha is not considered a hbond donor.
> > >>
> > >> Kind regards,
> > >> Erik
> > >> __
> > >> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> > >> Department of Chemistry – BMC, Uppsala University
> > >> +46 (0)18 471 4539
> > >> erik.markl...@kemi.uu.se > >> erik.markl...@kemi.uu.se>
> > >>
> > >> On 13 Mar 2018, at 11:03, Dilip H N  mailto:
> > >> cy16f01.di...@nitk.edu.in> > >> cy16f01.di...@nitk.edu.in>> wrote:
> > >>
> > >> Hello,
> > >> I want to calculate Hydrogen bonding between C-alpha of glycine and
> the
> > >> oxygen atom of water molecules.
> > >> So, i gave the command as:-
> > >>
> > >> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
> > >>
> > >> but i got the error as:
> > >> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
> > >> Found 0 donors and 511 acceptors
> > >> No Donors found
> > >> ---
> > >> Program: gmx hbond, version 2016.2
> > >> Source file: src/gromacs

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-14 Thread Dilip H N 
1) I tried with the Nitrogen atom of glycine and the oxygen atom of water
also using the command

gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -num abc.xvg

but still, i am getting the same error as:-
Specify 2 groups to analyze:
Group 0 (  N) has 1 elements
Group 1 ( OW) has   511 elements
Select a group: 0
Selected 0: 'N'
Select a group: 1
Selected 1: 'OW'
Checking for overlap in atoms between N and OW
Calculating hydrogen bonds between N (1 atoms) and OW (511 atoms)
Found 0 donors and 512 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

2) I tried to find out the distance between Calpha(Ca) and Ow from the
command
gmx hbond -f nptmd.trr -s nptmd.tpr -n NgOw.ndx -dist abc.xvg

but still, i am getting the same error as above one.

Any suggestions...

Thank you.

‌
 Sent with Mailtrack


On Tue, Mar 13, 2018 at 7:34 PM, Erik Marklund 
wrote:

> A shortcut would be to only look at the C-O distance, which can be done
> with gmx hbond without modification.
>
> Kind regards,
> Erik
>
> > On 13 Mar 2018, at 15:01, Jeremy T First 
> wrote:
> >
> > Hi Dilip,
> >
> > There is quite a bit of literature, especially recently, that considers
> the
> > alpha carbon as a hydrogen bond donor. How well this is represented in
> your
> > simulation will depend on your force field.
> >
> > You will likely need to develop your own gromacs tool to calculate this,
> > but it should be quite easy. We recently wrote a tool that does something
> > very similar, but you would need to edit it for your own purposes. If you
> > are interested in using our code as a template, feel free to contact me
> off
> > list.
> >
> > Good luck!
> > Jeremy
> >
> >
> >
> >
> > Jeremy Todd First
> > Webb Research Group
> > University of Texas at Austin
> > jeremy_fi...@utexas.edu
> > (443) 243-1187
> >
> > On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund  >
> > wrote:
> >
> >> The point is that Calpha don’t form hydrogen bonds.
> >>
> >> Erik
> >> __
> >> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> >> Department of Chemistry – BMC, Uppsala University
> >> +46 (0)18 471 4539
> >> erik.markl...@kemi.uu.se
> >>
> >> On 13 Mar 2018, at 13:20, Dilip H N  >> cy16f01.di...@nitk.edu.in>> wrote:
> >>
> >> Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
> >> atom of water molecules..??
> >> What are the other possible ways..??
> >>
> >>
> >>
> >>  Sent with Mailtrack
> >>  signature&utm_campaign=
> >> signaturevirality& >> gmail&utm_medium=signature&utm_campaign=signaturevirality&>>
> >>
> >> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund <
> erik.markl...@kemi.uu.se<
> >> mailto:erik.markl...@kemi.uu.se>>
> >> wrote:
> >>
> >> Dear Dilip,
> >>
> >> The Calpha is not considered a hbond donor.
> >>
> >> Kind regards,
> >> Erik
> >> __
> >> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> >> Department of Chemistry – BMC, Uppsala University
> >> +46 (0)18 471 4539
> >> erik.markl...@kemi.uu.se >> erik.markl...@kemi.uu.se>
> >>
> >> On 13 Mar 2018, at 11:03, Dilip H N  >> cy16f01.di...@nitk.edu.in> >> cy16f01.di...@nitk.edu.in>> wrote:
> >>
> >> Hello,
> >> I want to calculate Hydrogen bonding between C-alpha of glycine and the
> >> oxygen atom of water molecules.
> >> So, i gave the command as:-
> >>
> >> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
> >>
> >> but i got the error as:
> >> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
> >> Found 0 donors and 511 acceptors
> >> No Donors found
> >> ---
> >> Program: gmx hbond, version 2016.2
> >> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
> >> Fatal error:
> >> Nothing to be done
> >>
> >> So, how can i solve this issue..?? Is there no any Hydrogen bonding
> between
> >> this..?? (I think there is some hydrogen bonding present ...)
> >>
> >> Any suggestions are appreciated.
> >>
> >> Thank you.
> >>
> >> --
> >> With Best Regards,
> >>
> >> DILIP.H.N
> >> PhD Student
> >>
> >>
> >>
> >> ‌
> >>  Sent with Mailtrack
> >>  signature&utm_campaign=
> >> signaturevirality&>
> >> --
> >> 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

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Erik Marklund 
A shortcut would be to only look at the C-O distance, which can be done with 
gmx hbond without modification.

Kind regards,
Erik

> On 13 Mar 2018, at 15:01, Jeremy T First  wrote:
> 
> Hi Dilip,
> 
> There is quite a bit of literature, especially recently, that considers the
> alpha carbon as a hydrogen bond donor. How well this is represented in your
> simulation will depend on your force field.
> 
> You will likely need to develop your own gromacs tool to calculate this,
> but it should be quite easy. We recently wrote a tool that does something
> very similar, but you would need to edit it for your own purposes. If you
> are interested in using our code as a template, feel free to contact me off
> list.
> 
> Good luck!
> Jeremy
> 
> 
> 
> 
> Jeremy Todd First
> Webb Research Group
> University of Texas at Austin
> jeremy_fi...@utexas.edu
> (443) 243-1187
> 
> On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund 
> wrote:
> 
>> The point is that Calpha don’t form hydrogen bonds.
>> 
>> Erik
>> __
>> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
>> Department of Chemistry – BMC, Uppsala University
>> +46 (0)18 471 4539
>> erik.markl...@kemi.uu.se
>> 
>> On 13 Mar 2018, at 13:20, Dilip H N > cy16f01.di...@nitk.edu.in>> wrote:
>> 
>> Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
>> atom of water molecules..??
>> What are the other possible ways..??
>> 
>> 
>> 
>>  Sent with Mailtrack
>> > signaturevirality&> gmail&utm_medium=signature&utm_campaign=signaturevirality&>>
>> 
>> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund > mailto:erik.markl...@kemi.uu.se>>
>> wrote:
>> 
>> Dear Dilip,
>> 
>> The Calpha is not considered a hbond donor.
>> 
>> Kind regards,
>> Erik
>> __
>> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
>> Department of Chemistry – BMC, Uppsala University
>> +46 (0)18 471 4539
>> erik.markl...@kemi.uu.se> erik.markl...@kemi.uu.se>
>> 
>> On 13 Mar 2018, at 11:03, Dilip H N > cy16f01.di...@nitk.edu.in>> cy16f01.di...@nitk.edu.in>> wrote:
>> 
>> Hello,
>> I want to calculate Hydrogen bonding between C-alpha of glycine and the
>> oxygen atom of water molecules.
>> So, i gave the command as:-
>> 
>> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
>> 
>> but i got the error as:
>> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
>> Found 0 donors and 511 acceptors
>> No Donors found
>> ---
>> Program: gmx hbond, version 2016.2
>> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
>> Fatal error:
>> Nothing to be done
>> 
>> So, how can i solve this issue..?? Is there no any Hydrogen bonding between
>> this..?? (I think there is some hydrogen bonding present ...)
>> 
>> Any suggestions are appreciated.
>> 
>> Thank you.
>> 
>> --
>> With Best Regards,
>> 
>> DILIP.H.N
>> PhD Student
>> 
>> 
>> 
>> ‌
>>  Sent with Mailtrack
>> > signaturevirality&>
>> --
>> 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> gromacs.org>> gromacs.org>.
>> 
>> --
>> 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> gromacs.org>.
>> 
>> 
>> 
>> 
>> --
>> With Best Regards,
>> 
>> DILIP.H.N
>> Ph.D Student
>> --
>> 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> gromacs.org>.
>> 
>> --
>> 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

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Jeremy T First 
Hi Dilip,

There is quite a bit of literature, especially recently, that considers the
alpha carbon as a hydrogen bond donor. How well this is represented in your
simulation will depend on your force field.

You will likely need to develop your own gromacs tool to calculate this,
but it should be quite easy. We recently wrote a tool that does something
very similar, but you would need to edit it for your own purposes. If you
are interested in using our code as a template, feel free to contact me off
list.

Good luck!
Jeremy




Jeremy Todd First
Webb Research Group
University of Texas at Austin
jeremy_fi...@utexas.edu
(443) 243-1187

On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund 
wrote:

> The point is that Calpha don’t form hydrogen bonds.
>
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 13 Mar 2018, at 13:20, Dilip H N  cy16f01.di...@nitk.edu.in>> wrote:
>
> Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
> atom of water molecules..??
> What are the other possible ways..??
>
>
>
>  Sent with Mailtrack
>  signaturevirality& gmail&utm_medium=signature&utm_campaign=signaturevirality&>>
>
> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund  mailto:erik.markl...@kemi.uu.se>>
> wrote:
>
> Dear Dilip,
>
> The Calpha is not considered a hbond donor.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se erik.markl...@kemi.uu.se>
>
> On 13 Mar 2018, at 11:03, Dilip H N  cy16f01.di...@nitk.edu.in> cy16f01.di...@nitk.edu.in>> wrote:
>
> Hello,
> I want to calculate Hydrogen bonding between C-alpha of glycine and the
> oxygen atom of water molecules.
> So, i gave the command as:-
>
> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
>
> but i got the error as:
> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
> Found 0 donors and 511 acceptors
> No Donors found
> ---
> Program: gmx hbond, version 2016.2
> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
> Fatal error:
> Nothing to be done
>
> So, how can i solve this issue..?? Is there no any Hydrogen bonding between
> this..?? (I think there is some hydrogen bonding present ...)
>
> Any suggestions are appreciated.
>
> Thank you.
>
> --
> With Best Regards,
>
> DILIP.H.N
> PhD Student
>
>
>
> ‌
>  Sent with Mailtrack
>  signaturevirality&>
> --
> 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 gromacs.org> gromacs.org>.
>
> --
> 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 gromacs.org>.
>
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
> --
> 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 gromacs.org>.
>
> --
> 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.
>
-- 
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

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Erik Marklund 
The point is that Calpha don’t form hydrogen bonds.

Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 13 Mar 2018, at 13:20, Dilip H N 
mailto:cy16f01.di...@nitk.edu.in>> wrote:

Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
atom of water molecules..??
What are the other possible ways..??



 Sent with Mailtrack
>

On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund 
mailto:erik.markl...@kemi.uu.se>>
wrote:

Dear Dilip,

The Calpha is not considered a hbond donor.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 13 Mar 2018, at 11:03, Dilip H N 
mailto:cy16f01.di...@nitk.edu.in>mailto:cy16f01.di...@nitk.edu.in>>> wrote:

Hello,
I want to calculate Hydrogen bonding between C-alpha of glycine and the
oxygen atom of water molecules.
So, i gave the command as:-

gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg

but i got the error as:
Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
Found 0 donors and 511 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

So, how can i solve this issue..?? Is there no any Hydrogen bonding between
this..?? (I think there is some hydrogen bonding present ...)

Any suggestions are appreciated.

Thank you.

--
With Best Regards,

DILIP.H.N
PhD Student



‌
 Sent with Mailtrack

--
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>.

--
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.




--
With Best Regards,

DILIP.H.N
Ph.D Student
--
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.

-- 
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.

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Dilip H N 
Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
atom of water molecules..??
What are the other possible ways..??



 Sent with Mailtrack


On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund 
wrote:

> Dear Dilip,
>
> The Calpha is not considered a hbond donor.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 13 Mar 2018, at 11:03, Dilip H N  cy16f01.di...@nitk.edu.in>> wrote:
>
> Hello,
> I want to calculate Hydrogen bonding between C-alpha of glycine and the
> oxygen atom of water molecules.
> So, i gave the command as:-
>
> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
>
> but i got the error as:
> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
> Found 0 donors and 511 acceptors
> No Donors found
> ---
> Program: gmx hbond, version 2016.2
> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
> Fatal error:
> Nothing to be done
>
> So, how can i solve this issue..?? Is there no any Hydrogen bonding between
> this..?? (I think there is some hydrogen bonding present ...)
>
> Any suggestions are appreciated.
>
> Thank you.
>
> --
> With Best Regards,
>
> DILIP.H.N
> PhD Student
>
>
>
> ‌
>  Sent with Mailtrack
>  signaturevirality&>
> --
> 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 gromacs.org>.
>
> --
> 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.




-- 
With Best Regards,

DILIP.H.N
Ph.D Student
-- 
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.

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Erik Marklund 
Dear Dilip,

The Calpha is not considered a hbond donor.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 13 Mar 2018, at 11:03, Dilip H N 
mailto:cy16f01.di...@nitk.edu.in>> wrote:

Hello,
I want to calculate Hydrogen bonding between C-alpha of glycine and the
oxygen atom of water molecules.
So, i gave the command as:-

gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg

but i got the error as:
Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
Found 0 donors and 511 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

So, how can i solve this issue..?? Is there no any Hydrogen bonding between
this..?? (I think there is some hydrogen bonding present ...)

Any suggestions are appreciated.

Thank you.

--
With Best Regards,

DILIP.H.N
PhD Student



‌
 Sent with Mailtrack

--
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.

-- 
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.

[gmx-users] Regarding calculation of Hydrogen-Bond

2018-03-13 Thread Dilip H N 
Hello,
I want to calculate Hydrogen bonding between C-alpha of glycine and the
oxygen atom of water molecules.
So, i gave the command as:-

gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg

but i got the error as:
Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
Found 0 donors and 511 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

So, how can i solve this issue..?? Is there no any Hydrogen bonding between
this..?? (I think there is some hydrogen bonding present ...)

Any suggestions are appreciated.

Thank you.

-- 
With Best Regards,

DILIP.H.N
PhD Student



‌
 Sent with Mailtrack

-- 
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.