Re: [gmx-users] Grompp error on index file
Mr Bernard Ramos wrote:
Hi Justin,
Thanks for the immediate response. I apologize but I don't have with me
the mdp and the top files at the moment. But I will have it e-mailed
once I get back to my working gromacs computer.
Yes, as I remember, the [moleculetype] at the bottom of the topol.top
was able to identify it as a carbohydrate. In fact, the index.file
identified it as a carbohydrate. I borrowed the nvt.mdp from the
Lysozyme tutorial authored by you. Thanks.
Then that may be your problem. What's in your system? Do you have any protein?
If you don't, then you can't specify "protein" in the .mdp file. The problem
is not the index file, it's the .mdp file. In some cases, the error message
gives you the wrong impression; it really means that a group in the .mdp file
does not exist. In most cases, that means you need to create an index group to
accommodate the system. In other cases, it means you're using a group that is
simply not applicable.
-Justin
--- On *Tue, 5/31/11, Justin A. Lemkul //* wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] Grompp error on index file
To: "Discussion list for GROMACS users"
Date: Tuesday, May 31, 2011, 10:09 AM
Mr Bernard Ramos wrote:
> Hi everyone!
> I added a residue on the gromacs 4.5.3 I have. I followed the
instructions as indicated in the "Adding A Residue to a Force Field"
with this link
_http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue_.
I added the residue to residuetypes.dat and indicated it as a
carbohydrate. The topology in fact was able to write it down as a
carbohydrate.
>
Carbohydrates should be grouped into the "other" category; I'm not
sure "Carbohydrate" is a recognized type. What do you mean the
topology wrote it as a carbohydrate? Is that the [moleculetype]
name it was given the topology?
> __
> Generating a topology went well with pdb2gmx, editconf, genbox,
energy minimization. However, I encountered the following error when
I was about to do an NVT equilibration.
>
--
> Program grompp, VERSION 4.5.3
> Source code file: readir.c, line: 1316
> Fatal error:
> Group protein not found in indexfile.
> Maybe you have non-default groups in your mdp file, while not
using the '-n' option of grompp.
> In that case use the '-n'option.
>
--
> In response, I created an index file using make_ndx. The index
file was able to generate correctly the molecule indices and
identified it correctly as indicated in the residuetypes.dat and
carbohydrate.rtp
>
Your error does not appear to be connected to the carbohydrate at
all. The problem appears to be the use of "protein."
Capitalization shouldn't matter, so I'm not sure why grompp is
complaining.
> And then I tried (again) the following command:
> $ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o
nvt.tpr.
> It still generates the same error as above. Please help
>
Please provide your .mdp file and topology, if it is small enough to
paste into an email.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@g
Re: [gmx-users] Grompp error on index file
Hi Justin, Thanks for the immediate response. I apologize but I don't have with me the mdp and the top files at the moment. But I will have it e-mailed once I get back to my working gromacs computer. Yes, as I remember, the [moleculetype] at the bottom of the topol.top was able to identify it as a carbohydrate. In fact, the index.file identified it as a carbohydrate. I borrowed the nvt.mdp from the Lysozyme tutorial authored by you. Thanks. --- On Tue, 5/31/11, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] Grompp error on index file To: "Discussion list for GROMACS users" Date: Tuesday, May 31, 2011, 10:09 AM Mr Bernard Ramos wrote: > Hi everyone! > I added a residue on the gromacs 4.5.3 I have. I followed the instructions >as indicated in the "Adding A Residue to a Force Field" with this link >_http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue_. > I added the residue to residuetypes.dat and indicated it as a carbohydrate. >The topology in fact was able to write it down as a carbohydrate. > Carbohydrates should be grouped into the "other" category; I'm not sure "Carbohydrate" is a recognized type. What do you mean the topology wrote it as a carbohydrate? Is that the [moleculetype] name it was given the topology? > __ > Generating a topology went well with pdb2gmx, editconf, genbox, energy > minimization. However, I encountered the following error when I was about to > do an NVT equilibration. > >-- > Program grompp, VERSION 4.5.3 > Source code file: readir.c, line: 1316 > Fatal error: > Group protein not found in indexfile. > Maybe you have non-default groups in your mdp file, while not using the '-n' > option of grompp. > In that case use the '-n'option. > -- > In response, I created an index file using make_ndx. The index file was able >to generate correctly the molecule indices and identified it correctly as >indicated in the residuetypes.dat and carbohydrate.rtp > Your error does not appear to be connected to the carbohydrate at all. The problem appears to be the use of "protein." Capitalization shouldn't matter, so I'm not sure why grompp is complaining. > And then I tried (again) the following command: > $ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o nvt.tpr. > It still generates the same error as above. Please help > Please provide your .mdp file and topology, if it is small enough to paste into an email. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Grompp error on index file
Mr Bernard Ramos wrote: Hi everyone! I added a residue on the gromacs 4.5.3 I have. I followed the instructions as indicated in the "Adding A Residue to a Force Field" with this link _http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue_. I added the residue to residuetypes.dat and indicated it as a carbohydrate. The topology in fact was able to write it down as a carbohydrate. Carbohydrates should be grouped into the "other" category; I'm not sure "Carbohydrate" is a recognized type. What do you mean the topology wrote it as a carbohydrate? Is that the [moleculetype] name it was given the topology? __ Generating a topology went well with pdb2gmx, editconf, genbox, energy minimization. However, I encountered the following error when I was about to do an NVT equilibration. -- Program grompp, VERSION 4.5.3 Source code file: readir.c, line: 1316 Fatal error: Group protein not found in indexfile. Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n'option. -- In response, I created an index file using make_ndx. The index file was able to generate correctly the molecule indices and identified it correctly as indicated in the residuetypes.dat and carbohydrate.rtp Your error does not appear to be connected to the carbohydrate at all. The problem appears to be the use of "protein." Capitalization shouldn't matter, so I'm not sure why grompp is complaining. And then I tried (again) the following command: $ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o nvt.tpr. It still generates the same error as above. Please help Please provide your .mdp file and topology, if it is small enough to paste into an email. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Grompp error on index file
Hi everyone! I added a residue on the gromacs 4.5.3 I have. I followed the instructions as indicated in the "Adding A Residue to a Force Field" with this link http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue. I added the residue to residuetypes.dat and indicated it as a carbohydrate. The topology in fact was able to write it down as a carbohydrate. Generating a topology went well with pdb2gmx, editconf, genbox, energy minimization. However, I encountered the following error when I was about to do an NVT equilibration. -- Program grompp, VERSION 4.5.3 Source code file: readir.c, line: 1316 Fatal error: Group protein not found in indexfile. Maybe you have non-default groups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n'option. -- In response, I created an index file using make_ndx. The index file was able to generate correctly the molecule indices and identified it correctly as indicated in the residuetypes.dat and carbohydrate.rtp And then I tried (again) the following command: $ grompp -f nvt.mdp -c molecule.gro -n index.ndx -p topol.top -o nvt.tpr. It still generates the same error as above. Please help-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
