Re: [gmx-users] Problems using grompp and amber force field

2007-05-09 Thread root 
Hi,
Thanks everybody by the comments. 
There was a error in the include files of the topology: The itp file
generated by pdb2gmx program was localized in a different folder that
where we were running to the grompp program.

Mario

El mar, 08-05-2007 a las 02:05 +0100, TJ Piggot escribió:
> Hi,
> 
> With regards to the versions you are correct, ffamber_v3.3.1 is for use 
> with Gromacs 3.3.1. As for the error i would suggest you do what Mark says 
> and make sure all your inclusions are correct.  If you still can't find the 
> problem then you need to post some of your .top file so we can have a look 
> at it
> 
> Tom
> 
> --On 08 May 2007 10:53 +1000 Mark Abraham <[EMAIL PROTECTED]> wrote:
> 
> > root wrote:
> >> Dear GROMACS user:
> >>
> >> Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
> >> http://folding.stanford.edu and now I understand your comments.
> >> We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
> >> desapears, but the error messages is similar.
> >> (Fatal error:
> > Atoms in the .top are not numbered consecutively from 1
> >
> > ---
> >
> > We tested the dick.top file, and we verified that the atoms
>  are numbered
> > consecutively from 1 to 758.)
> >
> > Have you inspected the #included files as well? The way cpp works, any
> > file #included is literally dropped into its parent file, so if you had
> > something wrong in such an #inclusion you'd need to fix that.
> >
> > Mark
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> 
> --
> TJ Piggot
> [EMAIL PROTECTED]
> University of Bristol, UK.
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
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Re: [gmx-users] Problems using grompp and amber force field

2007-05-08 Thread Maik Goette 
Yes, the 3.3.1 amber-FFs should be used, because the implementation of 
the QM/MM parts changed the format in some FF-parameters files.


I would suggest, not to use the OPLS-DNA parameter set, because it isn't 
published, yet (as I know) and also uses RESP-charges, which may also be 
problematic with OPLS. Using the amber-port is, in my opinion, the best 
way to handle DNA/RNA (in GROMACS).


I fear, I can't really help you with your error, but did you try the 
amber99 FF? I use that and never ran into such errors. Did you had a 
look, if your total charge is more or less an integer? If not, one 
proton in your first base may be the wrong type...but this shouldn't 
result into your error.


Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


root wrote:

Dear GROMACS user:

Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
http://folding.stanford.edu and now I understand your comments.  
We tried with cpp = /lib/cpp -traditional in the mdp file. The warning

desapears, but the error messages is similar.
(Fatal error:

Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms

are numbered

consecutively from 1 to 758.)


We download the ffamber_v3.3.1-doc.tar.gz, that we considered that
correspond to the 3.3.1 version of GROMACS.
Is this correct?

Thanks in advance.

Mario
 
El lun, 07-05-2007 a las 23:17 +0200, Erik Marklund escribió:
As someone already mentioned, the following can be found among the  
AMBERport FAQ:


 >>
Why do I get a grompp warning "missing white space after `#define  
proper_*'?"
Set "cpp = /lib/cpp -traditional" in your .mdp file to remove these  
warnings, which result from the use of the N* atom type of the AMBER  
family of force fields and can be ignored.

<<

Did you try doing that?

Good luck!

/Erik

7 maj 2007 kl. 22.29 skrev root:

Hi,



I think if you set "cpp = /lib/cpp -traditional" in your .mdp file then
it 
should get rid of the warnings about "spaces are absent in target after
the 
name of macro". For more info see 
<http://folding.stanford.edu/ffamber/FAQ.html>



Tom



--On 07 May 2007 20:42 +0200 David van der Spoel
<[EMAIL PROTECTED]> 
wrote:

David and GROMACS users:
Sorry we changed the error message in ...

/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:  warning: spaces
are absent in target after the name of macro

because of the original message was in spanish.

We checked these files above. We run GROMACS in fedora 6.0
We analyzed the warning messages. They correspond to a format of
description of a dihedral angle. For example the 538:22 warning
 correspond to le line 538 column 22

 #define proper_X_CT_N*_X
 and there are a format problem with the * symbol.

 we don't know that to do still with this.


Thanks in advance

root wrote:
De:
David van der Spoel
<[EMAIL PROTECTED]>
   Responder a:
Discussion list for GROMACS users

          Para:
Discussion list for GROMACS users

Asunto:
Re: [gmx-users] Problems using
grompp and amber force field
 Fecha:
Mon, 07 May 2007 20:42:51 +0200
(15:42 ART)

The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format  
(with

the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle  
90 90

90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top

The output of the program indicate
...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21:
warning: spaces are absent in targe

Re: [gmx-users] Problems using grompp and amber force field

2007-05-07 Thread TJ Piggot 

Hi,

With regards to the versions you are correct, ffamber_v3.3.1 is for use 
with Gromacs 3.3.1. As for the error i would suggest you do what Mark says 
and make sure all your inclusions are correct.  If you still can't find the 
problem then you need to post some of your .top file so we can have a look 
at it


Tom

--On 08 May 2007 10:53 +1000 Mark Abraham <[EMAIL PROTECTED]> wrote:


root wrote:

Dear GROMACS user:

Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
http://folding.stanford.edu and now I understand your comments.
We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
desapears, but the error messages is similar.
(Fatal error:

Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms

are numbered

consecutively from 1 to 758.)


Have you inspected the #included files as well? The way cpp works, any
file #included is literally dropped into its parent file, so if you had
something wrong in such an #inclusion you'd need to fix that.

Mark
___
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--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
___
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Re: [gmx-users] Problems using grompp and amber force field

2007-05-07 Thread Mark Abraham 

root wrote:

Dear GROMACS user:

Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
http://folding.stanford.edu and now I understand your comments.  
We tried with cpp = /lib/cpp -traditional in the mdp file. The warning

desapears, but the error messages is similar.
(Fatal error:

Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms

are numbered

consecutively from 1 to 758.)


Have you inspected the #included files as well? The way cpp works, any 
file #included is literally dropped into its parent file, so if you had 
something wrong in such an #inclusion you'd need to fix that.


Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

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Re: [gmx-users] Problems using grompp and amber force field

2007-05-07 Thread root 
Dear GROMACS user:

Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
http://folding.stanford.edu and now I understand your comments.  
We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
desapears, but the error messages is similar.
(Fatal error:
> >> Atoms in the .top are not numbered consecutively from 1
> >>
> >> ---
> >>
> >> We tested the dick.top file, and we verified that the atoms
> > are numbered
> >> consecutively from 1 to 758.)

We download the ffamber_v3.3.1-doc.tar.gz, that we considered that
correspond to the 3.3.1 version of GROMACS.
Is this correct?

Thanks in advance.

Mario
 
El lun, 07-05-2007 a las 23:17 +0200, Erik Marklund escribió:
> As someone already mentioned, the following can be found among the  
> AMBERport FAQ:
> 
>  >>
> Why do I get a grompp warning "missing white space after `#define  
> proper_*'?"
> Set "cpp = /lib/cpp -traditional" in your .mdp file to remove these  
> warnings, which result from the use of the N* atom type of the AMBER  
> family of force fields and can be ignored.
> <<
> 
> Did you try doing that?
> 
> Good luck!
> 
> /Erik
> 
> 7 maj 2007 kl. 22.29 skrev root:
> 
> Hi,

>I think if you set "cpp = /lib/cpp -traditional" in your .mdp file then
>it 
>should get rid of the warnings about "spaces are absent in target after
>the 
>name of macro". For more info see 
><http://folding.stanford.edu/ffamber/FAQ.html>

>Tom

>--On 07 May 2007 20:42 +0200 David van der Spoel
><[EMAIL PROTECTED]> 
>wrote:
> > David and GROMACS users:
> > Sorry we changed the error message in ...
> >
> > /usr/local/gromacs/share/top/ffamber03bon.itp:541:22:  warning: spaces
> > are absent in target after the name of macro
> >
> > because of the original message was in spanish.
> >
> > We checked these files above. We run GROMACS in fedora 6.0
> > We analyzed the warning messages. They correspond to a format of
> > description of a dihedral angle. For example the 538:22 warning
> >  correspond to le line 538 column 22
> >
> >  #define proper_X_CT_N*_X
> >  and there are a format problem with the * symbol.
> >
> >  we don't know that to do still with this.
> >
> >
> > Thanks in advance
> >
> > root wrote:
> > De:
> > David van der Spoel
> > <[EMAIL PROTECTED]>
> >Responder a:
> > Discussion list for GROMACS users
> > 
> >   Para:
> > Discussion list for GROMACS users
> > 
> > Asunto:
> > Re: [gmx-users] Problems using
> > grompp and amber force field
> >  Fecha:
> > Mon, 07 May 2007 20:42:51 +0200
> > (15:42 ART)
> >
> > The procedure to simulate the DNA dodecamer was:
> >
> > 1) We generate the DNA topology and coordinates in gromacs format  
> > (with
> > the amber03 force field ) using the pdb2gmx program:
> >
> > pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce
> >
> > 2) and we obtain the box with the dodecamer plus water coordinates
> > using editconf and genbox:
> >
> > editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle  
> > 90 90
> > 90
> > genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top
> >
> > 3) with the files dick03.pdb and dick.top we run grompp:
> >
> > grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top
> >
> > The output of the program indicate
> > ...
> > creating statusfile for 1 node...
> >
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
> > checking input for internal consistency...
> > calling /usr/bin/cpp...
> > In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
> >  de dick.top:11:
> > /usr/local/gromacs/share/top/ffamber03bon.itp:538:22:
> > warning: spaces are absent in target after the name of macro
> > /usr/local/gromacs/share/top/ffamber03bon.itp:541:22:
> > warning: spaces are absent in target after the name of macro
> > /usr/local/gromacs/share/top/ffamber03bon.itp:543:22:
> > warning: spaces are absent in target after the name of macro
> > /usr/local/gromacs/share/top/ffamber03bon.itp:547:21:
> > warning: spaces are absent in target after the name of macro
> > /usr/local/gromacs/share/top/ffamber03bon

Re: [gmx-users] Problems using grompp and amber force field

2007-05-07 Thread Erik Marklund 
As someone already mentioned, the following can be found among the  
AMBERport FAQ:


>>
Why do I get a grompp warning "missing white space after `#define  
proper_*'?"
Set "cpp = /lib/cpp -traditional" in your .mdp file to remove these  
warnings, which result from the use of the N* atom type of the AMBER  
family of force fields and can be ignored.

<<

Did you try doing that?

Good luck!

/Erik

7 maj 2007 kl. 22.29 skrev root:


David and GROMACS users:
Sorry we changed the error message in ...

/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:  warning: spaces
are absent in target after the name of macro

because of the original message was in spanish.

We checked these files above. We run GROMACS in fedora 6.0
We analyzed the warning messages. They correspond to a format of
description of a dihedral angle. For example the 538:22 warning
 correspond to le line 538 column 22

 #define proper_X_CT_N*_X
 and there are a format problem with the * symbol.

 we don't know that to do still with this.


Thanks in advance

root wrote:
De:
David van der Spoel
<[EMAIL PROTECTED]>
   Responder a:
Discussion list for GROMACS users

  Para:
Discussion list for GROMACS users

            Asunto:
Re: [gmx-users] Problems using
grompp and amber force field
 Fecha:
Mon, 07 May 2007 20:42:51 +0200
(15:42 ART)

The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format  
(with

the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle  
90 90

90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top

The output of the program indicate
...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19:
warning: spaces are absent in target after the name of macro
processing topology...

check the files above. is the error message correct? then fix
it.

what kind of system are you running this on?


processing topology...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 758

Fatal error:
Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms

are numbered

consecutively from 1 to 758.
We analyzed the warning messages. They correspond to a format

of

desciption of a dihedral angle. For example the 538:22 warning
correspond to le line 538 column 22

#define proper_X_CT_N*_X
and there are a format problem with the * simbol.

we don't know that to do still with this.



Thanks in advance

Mario Campo and Griselda Corral
Fac. de Cs. Exactas y Naturales
UNLPam




___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at

http://www.gromacs.org/search before posting!

Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read

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--
David.
 
__ 
__

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL P

Re: [gmx-users] Problems using grompp and amber force field

2007-05-07 Thread root 
David and GROMACS users:
Sorry we changed the error message in ...

/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:  warning: spaces
are absent in target after the name of macro

because of the original message was in spanish.

We checked these files above. We run GROMACS in fedora 6.0
We analyzed the warning messages. They correspond to a format of
description of a dihedral angle. For example the 538:22 warning
 correspond to le line 538 column 22
 
 #define proper_X_CT_N*_X  
 and there are a format problem with the * symbol.
 
 we don't know that to do still with this.
 

Thanks in advance

root wrote:
De: 
David van der Spoel
<[EMAIL PROTECTED]>
   Responder a: 
Discussion list for GROMACS users

  Para: 
Discussion list for GROMACS users

Asunto: 
Re: [gmx-users] Problems using
grompp and amber force field
 Fecha: 
Mon, 07 May 2007 20:42:51 +0200
(15:42 ART)

The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format (with
the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle 90 90
90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top
 
The output of the program indicate
...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19: 
warning: spaces are absent in target after the name of macro
processing topology...

check the files above. is the error message correct? then fix
it.

what kind of system are you running this on?

> processing topology...
> Generated 2701 of the 2701 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 2701 of the 2701 1-4 parameter combinations
> ---
> Program grompp, VERSION 3.3.1
> Source code file: toppush.c, line: 758
> 
> Fatal error:
> Atoms in the .top are not numbered consecutively from 1
> 
> ---
> 
> We tested the dick.top file, and we verified that the atoms
are numbered
> consecutively from 1 to 758. 
> We analyzed the warning messages. They correspond to a format
of
> desciption of a dihedral angle. For example the 538:22 warning
> correspond to le line 538 column 22
> 
> #define proper_X_CT_N*_X  
> and there are a format problem with the * simbol.
> 
> we don't know that to do still with this.
> 
> 
> 
> Thanks in advance
>  
> Mario Campo and Griselda Corral
> Fac. de Cs. Exactas y Naturales
> UNLPam 
> 
> 
> 
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php


-- 
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Up

Re: [gmx-users] Problems using grompp and amber force field

2007-05-07 Thread TJ Piggot 

Hi,

I think if you set "cpp = /lib/cpp -traditional" in your .mdp file then it 
should get rid of the warnings about "spaces are absent in target after the 
name of macro". For more info see 



Tom

--On 07 May 2007 20:42 +0200 David van der Spoel <[EMAIL PROTECTED]> 
wrote:



root wrote:

Dear GROMACS user:
David and Mark, thanks by our comments, suggestions and questions. If
our response is confused, please require us copies of output files (or
fragment).

The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format (with
the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle 90 90
90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top

The output of the program indicate
...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21:
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19:
warning: spaces are absent in target after the name of macro


check the files above. is the error message correct? then fix it.

what kind of system are you running this on?


processing topology...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 758

Fatal error:
Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms are numbered
consecutively from 1 to 758.
We analyzed the warning messages. They correspond to a format of
desciption of a dihedral angle. For example the 538:22 warning
correspond to le line 538 column 22

# define proper_X_CT_N*_X
and there are a format problem with the * simbol.

we don't know that to do still with this.


Other coments: Previosly,  we consult the gromacs mailing list,
searching similar DNA simulation and finding suggest about the opls-na
and amber force field. Initially, we attempted to obtain a topology with
the opls-na force fied, but fequent error mesagges about the format of
the input file were generated. In consecuence, we thinked that there was
differences in the input format to the differente versions of the
gromacs package. Of course, it is only a hypothesis.

Thanks in advance

Mario Campo and Griselda Corral
Fac. de Cs. Exactas y Naturales
UNLPam




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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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Re: [gmx-users] Problems using grompp and amber force field

2007-05-07 Thread David van der Spoel 

root wrote:

Dear GROMACS user:
David and Mark, thanks by our comments, suggestions and questions. If
our response is confused, please require us copies of output files (or
fragment). 


The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format (with
the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle 90 90
90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top
 
The output of the program indicate

...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19: 
warning: spaces are absent in target after the name of macro


check the files above. is the error message correct? then fix it.

what kind of system are you running this on?


processing topology...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 758

Fatal error:
Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms are numbered
consecutively from 1 to 758. 
We analyzed the warning messages. They correspond to a format of

desciption of a dihedral angle. For example the 538:22 warning
correspond to le line 538 column 22

#define proper_X_CT_N*_X  
and there are a format problem with the * simbol.


we don't know that to do still with this.


Other coments: Previosly,  we consult the gromacs mailing list,
searching similar DNA simulation and finding suggest about the opls-na
and amber force field. Initially, we attempted to obtain a topology with
the opls-na force fied, but fequent error mesagges about the format of
the input file were generated. In consecuence, we thinked that there was
differences in the input format to the differente versions of the
gromacs package. Of course, it is only a hypothesis.

Thanks in advance
 
Mario Campo and Griselda Corral

Fac. de Cs. Exactas y Naturales
UNLPam 





___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php



--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

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[gmx-users] Problems using grompp and amber force field

2007-05-07 Thread root 
Dear GROMACS user:
David and Mark, thanks by our comments, suggestions and questions. If
our response is confused, please require us copies of output files (or
fragment). 

The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format (with
the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle 90 90
90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top
 
The output of the program indicate
...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19: 
warning: spaces are absent in target after the name of macro
processing topology...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
---
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 758

Fatal error:
Atoms in the .top are not numbered consecutively from 1

---

We tested the dick.top file, and we verified that the atoms are numbered
consecutively from 1 to 758. 
We analyzed the warning messages. They correspond to a format of
desciption of a dihedral angle. For example the 538:22 warning
correspond to le line 538 column 22

#define proper_X_CT_N*_X  
and there are a format problem with the * simbol.

we don't know that to do still with this.


Other coments: Previosly,  we consult the gromacs mailing list,
searching similar DNA simulation and finding suggest about the opls-na
and amber force field. Initially, we attempted to obtain a topology with
the opls-na force fied, but fequent error mesagges about the format of
the input file were generated. In consecuence, we thinked that there was
differences in the input format to the differente versions of the
gromacs package. Of course, it is only a hypothesis.

Thanks in advance
 
Mario Campo and Griselda Corral
Fac. de Cs. Exactas y Naturales
UNLPam 




___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php