Re: [gmx-users] Complication of errors, .itp file regarding

2017-12-17 Thread RAHUL SURESH 
On Mon, 18 Dec 2017 at 1:27 AM, Justin Lemkul  wrote:

>
>
> On 12/17/17 2:54 PM, RAHUL SURESH wrote:
> > Dear all
> >
> > I managed to overcome above errors by manually creating an .itp file from
> > the parameter file of ffTK. But i end up with 139 warnings stating
> >
> >
> >
> >
> > *"Too few parameters on line (source file
> >
> /home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp,
> > line 1841) "*
> > Going through previous threads, the error arise because I have used atom
> > type instead of numbers in bond and angle section of .itp file. To change
> > all the names to number is really a difficult task ( though not
> impossible
> > ) and take lot ground work and much much time. I would like to know if
> > something can be done actually to create an itp through some script which
> > are already available, rather dumping all my time over this renumbering
> > process. Please sort out some better way.
> >
>
> Sounds like you have a totally broken topology. Solve the first issue
> you posted and to which I responded; it's much simpler to deal with.


Dear Justin

I got the first issue solved and this is what I get now. Broken topology..?
I have actually manually written it.  Is there any other option to generate
the itp file from parameter file of ffTK?



>
> -Justin
>
> >
> >
> > On Mon, 18 Dec 2017 at 12:41 AM, Justin Lemkul  wrote:
> >
> >>
> >> On 12/17/17 8:18 AM, RAHUL SURESH wrote:
> >>> Dear all
> >>>
> >>> Let me put forth the thing first. I have generated the parameter file
> >> using
> >>> fftk(structure.par) and derived the respective topology
> >> file(structure.top)
> >>> using topotools of vmd. Now to get the itp fiule, I manually copied the
> >>> necessary data from structure.top and made structure.itp file.
> >>>
> >>> For the command
> >>> * "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
> >>>I get so many warning and errors.
> >>>
> >>> WARNING 1 [file THC.itp, line 3]:
> >>> Overriding atomtype CG2D1
> >>>
> >>> WARNING 31 [file THC.itp, line 37]:
> >>> Overriding Bond parameters.
> >>>
> >>> WARNING 35 [file THC.itp, line 111]:
> >>> Overriding U-B parameters.
> >>>
> >>> *69 warning messages*
> >>>
> >>> ERROR 1 [file THC.itp, line 158]:
> >>> Encountered a second block of parameters for dihedral type 9 for
> the
> >> same
> >>> atoms, with either different parameters and/or the first block has
> >>> multiple lines. This is not supported.
> >> The above errors are due to the fact that your molecule's .itp file
> >> includes parameters that are already part of the parent force field,
> >> hence grompp overrides them with the second instance. Don't do this. If
> >> an interaction is already specifically parametrized and is part of the
> >> force field, use it. Remove duplicated parameters from your .itp file.
> >>
> >>> *47 error messages*
> >>>
> >>> and finally
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> *Fatal error:number of coordinates in coordinate file (solv.gro,
> >>> 31285) does not match topology (alz.top, 31330)*
> >>> Please make it simple.
> >> The answer to this problem is always the same - incorrect bookkeeping.
> >> Check your work starting from addition of solvent and count how many of
> >> each species there are to make sure you've done things correctly.
> >>
> >> -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.
> >>
>
> --
> ==
>
> 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.
>
-- 
*Regards,*
*Rahul

Re: [gmx-users] Complication of errors, .itp file regarding

2017-12-17 Thread Justin Lemkul 



On 12/17/17 2:54 PM, RAHUL SURESH wrote:

Dear all

I managed to overcome above errors by manually creating an .itp file from
the parameter file of ffTK. But i end up with 139 warnings stating




*"Too few parameters on line (source file
/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp,
line 1841) "*
Going through previous threads, the error arise because I have used atom
type instead of numbers in bond and angle section of .itp file. To change
all the names to number is really a difficult task ( though not impossible
) and take lot ground work and much much time. I would like to know if
something can be done actually to create an itp through some script which
are already available, rather dumping all my time over this renumbering
process. Please sort out some better way.



Sounds like you have a totally broken topology. Solve the first issue 
you posted and to which I responded; it's much simpler to deal with.


-Justin




On Mon, 18 Dec 2017 at 12:41 AM, Justin Lemkul  wrote:



On 12/17/17 8:18 AM, RAHUL SURESH wrote:

Dear all

Let me put forth the thing first. I have generated the parameter file

using

fftk(structure.par) and derived the respective topology

file(structure.top)

using topotools of vmd. Now to get the itp fiule, I manually copied the
necessary data from structure.top and made structure.itp file.

For the command
* "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
   I get so many warning and errors.

WARNING 1 [file THC.itp, line 3]:
Overriding atomtype CG2D1

WARNING 31 [file THC.itp, line 37]:
Overriding Bond parameters.

WARNING 35 [file THC.itp, line 111]:
Overriding U-B parameters.

*69 warning messages*

ERROR 1 [file THC.itp, line 158]:
Encountered a second block of parameters for dihedral type 9 for the

same

atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

The above errors are due to the fact that your molecule's .itp file
includes parameters that are already part of the parent force field,
hence grompp overrides them with the second instance. Don't do this. If
an interaction is already specifically parametrized and is part of the
force field, use it. Remove duplicated parameters from your .itp file.


*47 error messages*

and finally





*Fatal error:number of coordinates in coordinate file (solv.gro,
31285) does not match topology (alz.top, 31330)*
Please make it simple.

The answer to this problem is always the same - incorrect bookkeeping.
Check your work starting from addition of solvent and count how many of
each species there are to make sure you've done things correctly.

-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
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posting!

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send a mail to gmx-users-requ...@gromacs.org.



--
==

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

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Re: [gmx-users] Complication of errors, .itp file regarding

2017-12-17 Thread RAHUL SURESH 
Dear all

I managed to overcome above errors by manually creating an .itp file from
the parameter file of ffTK. But i end up with 139 warnings stating




*"Too few parameters on line (source file
/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp,
line 1841) "*
Going through previous threads, the error arise because I have used atom
type instead of numbers in bond and angle section of .itp file. To change
all the names to number is really a difficult task ( though not impossible
) and take lot ground work and much much time. I would like to know if
something can be done actually to create an itp through some script which
are already available, rather dumping all my time over this renumbering
process. Please sort out some better way.




On Mon, 18 Dec 2017 at 12:41 AM, Justin Lemkul  wrote:

>
>
> On 12/17/17 8:18 AM, RAHUL SURESH wrote:
> > Dear all
> >
> > Let me put forth the thing first. I have generated the parameter file
> using
> > fftk(structure.par) and derived the respective topology
> file(structure.top)
> > using topotools of vmd. Now to get the itp fiule, I manually copied the
> > necessary data from structure.top and made structure.itp file.
> >
> > For the command
> > * "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
> >   I get so many warning and errors.
> >
> > WARNING 1 [file THC.itp, line 3]:
> >Overriding atomtype CG2D1
> >
> > WARNING 31 [file THC.itp, line 37]:
> >Overriding Bond parameters.
> >
> > WARNING 35 [file THC.itp, line 111]:
> >Overriding U-B parameters.
> >
> > *69 warning messages*
> >
> > ERROR 1 [file THC.itp, line 158]:
> >Encountered a second block of parameters for dihedral type 9 for the
> same
> >atoms, with either different parameters and/or the first block has
> >multiple lines. This is not supported.
>
> The above errors are due to the fact that your molecule's .itp file
> includes parameters that are already part of the parent force field,
> hence grompp overrides them with the second instance. Don't do this. If
> an interaction is already specifically parametrized and is part of the
> force field, use it. Remove duplicated parameters from your .itp file.
>
> > *47 error messages*
> >
> > and finally
> >
> >
> >
> >
> >
> > *Fatal error:number of coordinates in coordinate file (solv.gro,
> > 31285) does not match topology (alz.top, 31330)*
> > Please make it simple.
>
> The answer to this problem is always the same - incorrect bookkeeping.
> Check your work starting from addition of solvent and count how many of
> each species there are to make sure you've done things correctly.
>
> -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.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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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Re: [gmx-users] Complication of errors, .itp file regarding

2017-12-17 Thread Justin Lemkul 



On 12/17/17 8:18 AM, RAHUL SURESH wrote:

Dear all

Let me put forth the thing first. I have generated the parameter file using
fftk(structure.par) and derived the respective topology file(structure.top)
using topotools of vmd. Now to get the itp fiule, I manually copied the
necessary data from structure.top and made structure.itp file.

For the command
* "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
  I get so many warning and errors.

WARNING 1 [file THC.itp, line 3]:
   Overriding atomtype CG2D1

WARNING 31 [file THC.itp, line 37]:
   Overriding Bond parameters.

WARNING 35 [file THC.itp, line 111]:
   Overriding U-B parameters.

*69 warning messages*

ERROR 1 [file THC.itp, line 158]:
   Encountered a second block of parameters for dihedral type 9 for the same
   atoms, with either different parameters and/or the first block has
   multiple lines. This is not supported.


The above errors are due to the fact that your molecule's .itp file 
includes parameters that are already part of the parent force field, 
hence grompp overrides them with the second instance. Don't do this. If 
an interaction is already specifically parametrized and is part of the 
force field, use it. Remove duplicated parameters from your .itp file.



*47 error messages*

and finally





*Fatal error:number of coordinates in coordinate file (solv.gro,
31285) does not match topology (alz.top, 31330)*
Please make it simple.


The answer to this problem is always the same - incorrect bookkeeping. 
Check your work starting from addition of solvent and count how many of 
each species there are to make sure you've done things correctly.


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

Re: [gmx-users] Complication of errors, .itp file regarding

2017-12-17 Thread RAHUL SURESH 
Dear all

I managed to overcome above errors by manually creating an .itp file from
the parameter file of ffTK. But i end up with 139 warnings stating




*"Too few parameters on line (source file
/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp,
line 1841) "*
Going through previous threads, the error arise because I have used atom
type instead of numbers in bond and angle section of .itp file. To change
all the names to number is really a difficult task ( though not impossible
) and take lot ground work and much much time. I would like to know if
something can be done actually to create an itp through some script which
are already available, rather dumping all my time over this renumbering
process. Please sort out some better way.

On Sun, Dec 17, 2017 at 6:48 PM, RAHUL SURESH 
wrote:

> Dear all
>
> Let me put forth the thing first. I have generated the parameter file
> using fftk(structure.par) and derived the respective topology
> file(structure.top) using topotools of vmd. Now to get the itp fiule, I
> manually copied the necessary data from structure.top and made
> structure.itp file.
>
> For the command
> * "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
>  I get so many warning and errors.
>
> WARNING 1 [file THC.itp, line 3]:
>   Overriding atomtype CG2D1
>
> WARNING 31 [file THC.itp, line 37]:
>   Overriding Bond parameters.
>
> WARNING 35 [file THC.itp, line 111]:
>   Overriding U-B parameters.
>
> *69 warning messages*
>
> ERROR 1 [file THC.itp, line 158]:
>   Encountered a second block of parameters for dihedral type 9 for the same
>   atoms, with either different parameters and/or the first block has
>   multiple lines. This is not supported.
>
> *47 error messages*
>
> and finally
>
>
>
>
>
> *Fatal error:number of coordinates in coordinate file (solv.gro,
> 31285) does not match topology (alz.top, 31330)*
> Please make it simple.
>
>
>
>
>
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>



-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Complication of errors, .itp file regarding

2017-12-17 Thread RAHUL SURESH 
Dear all

Let me put forth the thing first. I have generated the parameter file using
fftk(structure.par) and derived the respective topology file(structure.top)
using topotools of vmd. Now to get the itp fiule, I manually copied the
necessary data from structure.top and made structure.itp file.

For the command
* "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
 I get so many warning and errors.

WARNING 1 [file THC.itp, line 3]:
  Overriding atomtype CG2D1

WARNING 31 [file THC.itp, line 37]:
  Overriding Bond parameters.

WARNING 35 [file THC.itp, line 111]:
  Overriding U-B parameters.

*69 warning messages*

ERROR 1 [file THC.itp, line 158]:
  Encountered a second block of parameters for dihedral type 9 for the same
  atoms, with either different parameters and/or the first block has
  multiple lines. This is not supported.

*47 error messages*

and finally





*Fatal error:number of coordinates in coordinate file (solv.gro,
31285) does not match topology (alz.top, 31330)*
Please make it simple.








-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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
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