Sorry for the mistake..
It worked well!!!
Thank you...
Aswathy
Dept. Biotechnology
Ext. 3108
----- Original Message -----
From: gmx-users-requ...@gromacs.org
To: gmx-users@gromacs.org
Sent: Tuesday, February 3, 2009 1:47:57 PM GMT +05:30 Chennai, Kolkata, Mumbai,
New Delhi
Subject: gmx-users Digest, Vol 58, Issue 16
Send gmx-users mailing list submissions to
gmx-users@gromacs.org
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. Re: Re: IN4 molecule type error (Justin A. Lemkul)
2. Re: Re: IN4 molecule type error (Mark Abraham)
3. Re: Re: IN4 molecule type error (Mark Abraham)
4. free energy decomposition (friendli)
----------------------------------------------------------------------
Message: 1
Date: Mon, 02 Feb 2009 22:13:23 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] Re: IN4 molecule type error
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4987b653.8090...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed
Ms. Aswathy S wrote:
> Hi,
>
> I have added the #include "drg.itp" statement under the title, ; Include
> forcefield parameters in the .top file. Thr drg.itp is saved in the current
> directory.
>
This is the incorrect order. You've inserted the drg.itp moleculetype
information before your protein, then called the protein before IN4 in the [
molecules ] section. Order is important. Include the moleculetypes in the
order that they appear in the structure file (.pdb or .gro). See a few
comments
embedded below.
> Still showing the sanme error as previous.
>
> including a part of the top file.Please check this.
> ________________________________________
> ; This is your topology file
> ; TRYPSIN
> ;
> ; Include forcefield parameters
> #include "ffgmx.itp"
> #include�� "drg.itp"��
>
I don't know if this is just strange behavior from my email client, but if
you've got these hidden characters within this line of text, it will not be
interpreted correctly. Make sure you are using a plain text editor, like vi or
emacs, to edit your topology file.
> [ moleculetype ]
> ; Name nrexcl
> Protein_A 3
> ____________________________________________
>
> At the end,
> ____________________________________________
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
* This is where you should #include "drg.itp" *
The position restraint information relates to the protein moleculetype
definition, therefore ending the information for this particular molecule.
I suggest a thorough read of Chapter 5 to become more familiar with the Gromacs
topology structure. I believe this information is explained in John Kerrigan's
tutorial, as well.
-Justin
> ; Include water topology
> #include "spce.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> TRYPSIN in water
>
> [ molecules ]
> ; Compound #mols
> Protein_A 1
> IN4 1
> SOL 8902
> ___________________________________________
>
> Thanks,
> Aswathy
> Dept. Biotechnology
> Ext. 3108
>
> ----- Original Message -----
> From: gmx-users-requ...@gromacs.org
> To: gmx-users@gromacs.org
> Sent: Sunday, February 1, 2009 9:28:44 PM GMT +05:30 Chennai, Kolkata,
> Mumbai, New Delhi
> Subject: gmx-users Digest, Vol 58, Issue 3
>
> Send gmx-users mailing list submissions to
> gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
> gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: gmx-users Digest, Vol 58, Issue 2 (Ms. Aswathy S)
> 2. RE: Re: gmx-users Digest, Vol 58, Issue 2 (Mohammed Kamal)
> 3. Re: COM motion removal (Mark Abraham)
> 4. infinite polymer crystals at gromacs 4.x.x (Claus Valka)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 1 Feb 2009 16:49:17 +0530 (IST)
> From: "Ms. Aswathy S" <aswat...@amritapuri.amrita.edu>
> Subject: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 2
> To: gmx-users@gromacs.org
> Message-ID:
> <7604642.142011233487157801.javamail.r...@durga.amrita.ac.in>
> Content-Type: text/plain; charset=utf-8
>
> Dear Mohammed,
>
> Thanks for your reply.
> The .ITP file from the PRODRG server has saved as drg.itp and added "#include
> "drg.itp"" line in the topology file.
> still getting the same error.
>
> Where should I save the drg.itp file in the present working directory or
> share/top directory?
>
> Thanks,
> Aswathy
> Dept. Biotechnology
> Ext. 3108
>
> ----- Original Message -----
> From: gmx-users-requ...@gromacs.org
> To: gmx-users@gromacs.org
> Sent: Sunday, February 1, 2009 4:30:04 PM GMT +05:30 Chennai, Kolkata,
> Mumbai, New Delhi
> Subject: gmx-users Digest, Vol 58, Issue 2
>
> Send gmx-users mailing list submissions to
> gmx-users@gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-requ...@gromacs.org
>
> You can reach the person managing the list at
> gmx-users-ow...@gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. RE: IN4 molecule type error (Mohammed Kamal)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 1 Feb 2009 21:11:11 +1100
> From: Mohammed Kamal <mohkam...@hotmail.com>
> Subject: RE: [gmx-users] IN4 molecule type error
> To: Gromacs <gmx-users@gromacs.org>
> Message-ID: <bay118-w17cc364801c129280ea54ef4...@phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> You have to include the .itp file that you have obtained from PRODRG in the
> topology file. Be sure that you have changed the extension of the .itp file
> that you have obtained from the PRODRG server from .ITP to .itp!!
> Mohammed
>
>> Date: Fri, 30 Jan 2009 20:57:28 +0530
>> From: aswat...@amritapuri.amrita.edu
>> To: gmx-users@gromacs.org
>> Subject: [gmx-users] IN4 molecule type error
>>
>> Dear Gromacs users,
>>
>> I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial
>> for a test run and i have ended up with following error. Please try to help
>> me
>>
>>
>> creating statusfile for 1 node...
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90#
>> checking input for internal consistency...
>> calling /usr/bin/cpp...
>> TEST1/trp.top:12:9: error: #include expects "FILENAME" or <FILENAME>
>> cpp exit code: 256
>> Tried to execute: '/usr/bin/cpp -I/usr/local/gromacs/share/top -DFLEXIBLE
>> TEST1/trp.top > gromppVEFM2b'
>> The '/usr/bin/cpp' command is defined in the .mdp file
>> processing topology...
>> Generated 1284 of the 1485 non-bonded parameter combinations
>> Excluding 3 bonded neighbours for Protein_A 1
>> Cleaning up temporary file gromppVEFM2b
>> Fatal error: No such moleculetype IN4
>>
>> Can you please tell me what could be the reason for this? Please help me.
>>
>> Thanks in advance,
>>
>> Aswathy
>> Amrita School of Biotechnology
>> Dept. Biotechnology
>> Ext. 3108
>> _______________________________________________
>> gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> _________________________________________________________________
> Get rid of those unwanted christmas presents! Get what you want at ebay.
> http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Frover%2Eebay%2Ecom%2Frover%2F1%2F705%2D10129%2D5668%2D323%2F4%3Fid%3D10&_t=763807330&_r=hotmailTAGLINES&_m=EXT
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> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 58, Issue 2
> ****************************************
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 1 Feb 2009 22:31:53 +1100
> From: Mohammed Kamal <mohkam...@hotmail.com>
> Subject: RE: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 2
> To: Gromacs <gmx-users@gromacs.org>
> Message-ID: <bay118-w46c2f7a7f15c99905dc7dbf4...@phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Saving it in the working directory should work fine..... I hope that you have
> added the #include line in the right place within the topology file
> Mohammed
>
>> Date: Sun, 1 Feb 2009 16:49:17 +0530
>> From: aswat...@amritapuri.amrita.edu
>> To: gmx-users@gromacs.org
>> Subject: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 2
>>
>> Dear Mohammed,
>>
>> Thanks for your reply.
>> The .ITP file from the PRODRG server has saved as drg.itp and added
>> "#include "drg.itp"" line in the topology file.
>> still getting the same error.
>>
>> Where should I save the drg.itp file in the present working directory or
>> share/top directory?
>>
>> Thanks,
>> Aswathy
>> Dept. Biotechnology
>> Ext. 3108
>>
>> ----- Original Message -----
>> From: gmx-users-requ...@gromacs.org
>> To: gmx-users@gromacs.org
>> Sent: Sunday, February 1, 2009 4:30:04 PM GMT +05:30 Chennai, Kolkata,
>> Mumbai, New Delhi
>> Subject: gmx-users Digest, Vol 58, Issue 2
>>
>> Send gmx-users mailing list submissions to
>> gmx-users@gromacs.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> or, via email, send a message with subject or body 'help' to
>> gmx-users-requ...@gromacs.org
>>
>> You can reach the person managing the list at
>> gmx-users-ow...@gromacs.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of gmx-users digest..."
>>
>>
>> Today's Topics:
>>
>> 1. RE: IN4 molecule type error (Mohammed Kamal)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sun, 1 Feb 2009 21:11:11 +1100
>> From: Mohammed Kamal <mohkam...@hotmail.com>
>> Subject: RE: [gmx-users] IN4 molecule type error
>> To: Gromacs <gmx-users@gromacs.org>
>> Message-ID: <bay118-w17cc364801c129280ea54ef4...@phx.gbl>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> You have to include the .itp file that you have obtained from PRODRG in the
>> topology file. Be sure that you have changed the extension of the .itp file
>> that you have obtained from the PRODRG server from .ITP to .itp!!
>> Mohammed
>>
>>> Date: Fri, 30 Jan 2009 20:57:28 +0530
>>> From: aswat...@amritapuri.amrita.edu
>>> To: gmx-users@gromacs.org
>>> Subject: [gmx-users] IN4 molecule type error
>>>
>>> Dear Gromacs users,
>>>
>>> I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial
>>> for a test run and i have ended up with following error. Please try to help
>>> me
>>>
>>>
>>> creating statusfile for 1 node...
>>>
>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90#
>>> checking input for internal consistency...
>>> calling /usr/bin/cpp...
>>> TEST1/trp.top:12:9: error: #include expects "FILENAME" or <FILENAME>
>>> cpp exit code: 256
>>> Tried to execute: '/usr/bin/cpp -I/usr/local/gromacs/share/top -DFLEXIBLE
>>> TEST1/trp.top > gromppVEFM2b'
>>> The '/usr/bin/cpp' command is defined in the .mdp file
>>> processing topology...
>>> Generated 1284 of the 1485 non-bonded parameter combinations
>>> Excluding 3 bonded neighbours for Protein_A 1
>>> Cleaning up temporary file gromppVEFM2b
>>> Fatal error: No such moleculetype IN4
>>>
>>> Can you please tell me what could be the reason for this? Please help me.
>>>
>>> Thanks in advance,
>>>
>>> Aswathy
>>> Amrita School of Biotechnology
>>> Dept. Biotechnology
>>> Ext. 3108
>>> _______________________________________________
>>> gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> _________________________________________________________________
>> Get rid of those unwanted christmas presents! Get what you want at ebay.
>> http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Frover%2Eebay%2Ecom%2Frover%2F1%2F705%2D10129%2D5668%2D323%2F4%3Fid%3D10&_t=763807330&_r=hotmailTAGLINES&_m=EXT
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>>
>> End of gmx-users Digest, Vol 58, Issue 2
>> ****************************************
>> _______________________________________________
>> gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> _________________________________________________________________
> Get rid of those unwanted christmas presents! Get what you want at ebay.
> http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Frover%2Eebay%2Ecom%2Frover%2F1%2F705%2D10129%2D5668%2D323%2F4%3Fid%3D10&_t=763807330&_r=hotmailTAGLINES&_m=EXT
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> ------------------------------
>
> Message: 3
> Date: Sun, 01 Feb 2009 22:59:14 +1100
> From: Mark Abraham <mark.abra...@anu.edu.au>
> Subject: Re: [gmx-users] COM motion removal
> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Message-ID: <fc8e8051d35.49862...@anu.edu.au>
> Content-Type: text/plain; charset=us-ascii
>
> ----- Original Message -----
> From: priyanka srivastava <priyanka...@yahoo.com>
> Date: Saturday, January 31, 2009 10:20 pm
> Subject: [gmx-users] COM motion removal
> To: gmx-users@gromacs.org
>
>> Dear Gromacs users!!
>>
>> I have a lipid - peptide system which I simulated for 50ns. Now in the
>> beginning of the simulation the peptide was at the center of the bilayer but
>> with time the peptide moved and came very close to the edge. Now near the
>> edge it is having the interactions with the images of the lipid bilayer,
>> since pbc is on, but when I view it using ngmx then the peptide appears to
>> be lying near the edge.
>
> If your peptide atoms can see both sides of the bilayer, then your lipid
> headgroups can also see their counterparts and you are not simulating a
> bilayer.
>
> I am not sure what you think your issue is... you say the peptide "came very
> close to the edge" and then "appears to be lying near the edge".
>
>> Is there any way by which I can write the coordinates of the images of the
>> lipid bilayer since pbc is on?Using trjconv is not helping me since it moves
>> the entire system i.e. lipid bilayer+water+peptide. So what I am looking for
>> is an option to get the images atoms so that the environment of the peptide
>> remains same and at the same time the peptide is positioned near the center
>> of the box.
>
> As Justin said, you should consult the other possibilities trjconv permits
> and be prepared to try a few iterates with different options to see what they
> do.
>
> You can't force the "environment of the peptide" to remain the same - you are
> sampling from a heterogenous simulation environment. If it moved from the
> centre of the bilayer then postprocessing won't move it back.
>
>> Also I carried out an analysis in which I calculated number of water
>> molecules around residue 1 which is actually lying very close to the edge
>> (rather outside). I think if the pbc is on then the images are taken care of
>> automatically and it will already construct image boxes around those
>> residues which are close to the edge and then perform the number of water
>> molecules around residue 1 calculation?
>
> PBC will be taken care of. You can verify this by counting a single example
> (approximately) by hand.
>
> Mark
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 1 Feb 2009 07:52:19 -0800 (PST)
> From: Claus Valka <lastexile...@yahoo.de>
> Subject: [gmx-users] infinite polymer crystals at gromacs 4.x.x
> To: gmx-users@gromacs.org
> Message-ID: <247940.82718...@web24609.mail.ird.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,back in gromacs versions 3.x.x there was the ability to simulate
> (polymer) crystals by enabling the option pbc = full in the mdp file.That way
> someone was avoiding the inconsistent shifts message and was able to simulate
> infinite systems.My question is: now in gromacs versions 4.0 and on, is this
> feature abandoned?������The screw option, which is new, I do not think that
> replaces the full option. The full option is no longer selectable. Is there
> any other way? Or in order to use the files we were using we have to stick
> with older versions?Yours Sincerely,Nikos
>
>
>
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> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 58, Issue 3
> ****************************************
> _______________________________________________
> gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 2
Date: Tue, 03 Feb 2009 14:15:50 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Re: IN4 molecule type error
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4987b6e6.6060...@anu.edu.au>
Content-Type: text/plain; charset=UTF-8; format=flowed
Ms. Aswathy S wrote:
> Hi,
>
> I have added the #include "drg.itp" statement under the title, ; Include
> forcefield parameters in the .top file. Thr drg.itp is saved in the current
> directory.
>
> Still showing the sanme error as previous.
>
> including a part of the top file.Please check this.
> ________________________________________
> ; This is your topology file
> ; TRYPSIN
> ;
> ; Include forcefield parameters
> #include "ffgmx.itp"
> #include�� "drg.itp"��
This line is your problem. Computers are literal, and they do not cope
magically with cruft created by (for example) cutting and pasting HTML
or editors that use proprietary document formats. The error message
> > TEST1/trp.top:12:9: error: #include expects "FILENAME" or <FILENAME>
was telling you this.
To first order, anything that comes on a Microsoft CD should not be used
for computational chemistry. :-)
Mark
------------------------------
Message: 3
Date: Tue, 03 Feb 2009 14:33:59 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Re: IN4 molecule type error
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4987bb27.1000...@anu.edu.au>
Content-Type: text/plain; charset=UTF-8; format=flowed
Justin A. Lemkul wrote:
>
>
> Ms. Aswathy S wrote:
>> Hi,
>>
>> I have added the #include "drg.itp" statement under the title, ;
>> Include forcefield parameters in the .top file. Thr drg.itp is saved
>> in the current directory.
>>
>
> This is the incorrect order. You've inserted the drg.itp moleculetype
> information before your protein, then called the protein before IN4 in
> the [ molecules ] section. Order is important. Include the
> moleculetypes in the order that they appear in the structure file (.pdb
> or .gro).
Order is important *within the [molecules] directive*. This order must
match the intended coordinate file. I don't believe order of the
[moleculetype] directives is pertinent; chapter 5 doesn't say it is, and
if it were, the names would be redundant. One could test this by
juggling the order of water #include directives in some topology. The
first system that came to hand proved this to be true.
>> Still showing the sanme error as previous.
>>
>> including a part of the top file.Please check this.
>> ________________________________________
>> ; This is your topology file
>> ; TRYPSIN
>> ;
>> ; Include forcefield parameters
>> #include "ffgmx.itp"
>> #include�� "drg.itp"��
>
> I don't know if this is just strange behavior from my email client, but
> if you've got these hidden characters within this line of text, it will
> not be interpreted correctly. Make sure you are using a plain text
> editor, like vi or emacs, to edit your topology file.
Hear, hear.
Mark
------------------------------
Message: 4
Date: Tue, 03 Feb 2009 16:16:55 +0800
From: friendli <friendli2...@gmail.com>
Subject: [gmx-users] free energy decomposition
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4987fd77.8000...@gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear all,
Does Gmx provide the functions to decompose the free energy calculated
using TI into various components, such as electrostatic, VDW, covalent
or contribution from each residue?
If it has, where can I find the procedures to do it?
thanks a lot
Qiang
------------------------------
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End of gmx-users Digest, Vol 58, Issue 16
*****************************************
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