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"Â
[ moleculetype ]
; Name nrexcl
Protein_A 3
____________________________________________
At the end,
____________________________________________
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; 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,
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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
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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
_________________________________________________________________
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------------------------------
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
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> 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
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_________________________________________________________________
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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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