Re: [gmx-users] Re: IN4 molecule type error

Mon, 02 Feb 2009 19:14:53 -0800 


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

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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

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To: gmx-users@gromacs.org
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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
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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

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        gmx-users@gromacs.org

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        http://www.gromacs.org/mailman/listinfo/gmx-users
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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
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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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--
========================================

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

========================================
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