[gmx-users] Re: IN4 molecule type error
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 3 04:13:23 CET 2009
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"Â
>
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-request at gromacs.org
> To: gmx-users at 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 at 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-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at 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" <aswathys at amritapuri.amrita.edu>
> Subject: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 2
> To: gmx-users at gromacs.org
> Message-ID:
> <7604642.142011233487157801.JavaMail.root at 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-request at gromacs.org
> To: gmx-users at 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 at 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-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at 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 <mohkam978 at hotmail.com>
> Subject: RE: [gmx-users] IN4 molecule type error
> To: Gromacs <gmx-users at gromacs.org>
> Message-ID: <BAY118-W17CC364801C129280EA54EF4C40 at 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: aswathys at amritapuri.amrita.edu
>> To: gmx-users at 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 at 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-request at 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 --------------
> An HTML attachment was scrubbed...
> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090201/800342b2/attachment-0001.html
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at 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 <mohkam978 at hotmail.com>
> Subject: RE: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 2
> To: Gromacs <gmx-users at gromacs.org>
> Message-ID: <BAY118-W46C2F7A7F15C99905DC7DBF4C40 at 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: aswathys at amritapuri.amrita.edu
>> To: gmx-users at 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-request at gromacs.org
>> To: gmx-users at 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 at 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-request at gromacs.org
>>
>> You can reach the person managing the list at
>> gmx-users-owner at 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 <mohkam978 at hotmail.com>
>> Subject: RE: [gmx-users] IN4 molecule type error
>> To: Gromacs <gmx-users at gromacs.org>
>> Message-ID: <BAY118-W17CC364801C129280EA54EF4C40 at 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: aswathys at amritapuri.amrita.edu
>>> To: gmx-users at 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 at 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-request at 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 --------------
>> An HTML attachment was scrubbed...
>> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090201/800342b2/attachment-0001.html
>>
>> ------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at 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 at 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-request at 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 --------------
> An HTML attachment was scrubbed...
> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090201/8dd1e969/attachment-0001.html
>
> ------------------------------
>
> Message: 3
> Date: Sun, 01 Feb 2009 22:59:14 +1100
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] COM motion removal
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fc8e8051d35.49862942 at anu.edu.au>
> Content-Type: text/plain; charset=us-ascii
>
> ----- Original Message -----
> From: priyanka srivastava <priyankaps4 at yahoo.com>
> Date: Saturday, January 31, 2009 10:20 pm
> Subject: [gmx-users] COM motion removal
> To: gmx-users at 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 <lastexile7gr at yahoo.de>
> Subject: [gmx-users] infinite polymer crystals at gromacs 4.x.x
> To: gmx-users at gromacs.org
> Message-ID: <247940.82718.qm at 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
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090201/dd7c416b/attachment.html
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at 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 at 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-request at 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
========================================
More information about the gromacs.org_gmx-users
mailing list