Re: [gmx-users] charmm gui pdb to gro

[Yogesh Sharma]

*thanks sahil *
*but i am interested in lipid molecule conversion not protein. I think
pdb2gmx will work for protein molecules only.*
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] charmm gui pdb to gro.

[Sahil Lall]

Hey, 

You could use pdb2gmx on the CHARMM-GUI ".pdb" output. The -ignh flag
allows for ignoring preexisting hydrogen atoms if that's really
required. 

Cheers, 

Sahil

On 2020-01-14 12:23, Yogesh Sharma wrote:

> Greetings,
> hey, I want to convert the charmm gui generated pdb (membrane + protein) to
> gromacs readable file.  charmm generated lipids contain hydrogen atoms and
> naming differences. I tried doing it manually but couldnt succeed. Is there
> any script available for atom renaming and reordering?
> 
> I also tried manual packing of POPC molecules from this site (
> http://wcm.ucalgary.ca/tieleman/downloads) around oriented protein
> extracted from charmm gui bilayer builder but simulation was not successful
> probably i couldnot pack it properly (didn't get any error though. packing
> was performed using inflategro with shrinking to a final area of 74A^2).
> Charmm gui generated output is working fine with water but I want to
> perform complete simulation in 54A7 ff due to ligand parameters
> availability. hence, i have to convert charmm gui generated output to gro
> format. Is there any way around?
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] charmm gui pdb to gro.

[Yogesh Sharma]

Greetings,
hey, I want to convert the charmm gui generated pdb (membrane + protein) to
gromacs readable file.  charmm generated lipids contain hydrogen atoms and
naming differences. I tried doing it manually but couldnt succeed. Is there
any script available for atom renaming and reordering?

I also tried manual packing of POPC molecules from this site (
http://wcm.ucalgary.ca/tieleman/downloads) around oriented protein
extracted from charmm gui bilayer builder but simulation was not successful
probably i couldnot pack it properly (didn't get any error though. packing
was performed using inflategro with shrinking to a final area of 74A^2).
Charmm gui generated output is working fine with water but I want to
perform complete simulation in 54A7 ff due to ligand parameters
availability. hence, i have to convert charmm gui generated output to gro
format. Is there any way around?
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CHARMM GUI membrane builder's assembled output

[Justin Lemkul]

On 9/19/19 2:24 PM, Yogesh Sharma wrote:

Greetings,
I used charmm gui's custom Membrane/protein builder to assemble components
for MD simulation. It gave me equillibriated box. I am confused whether I
should equllibriate box again or not? From which step should I start in
Gromac,Energy minimization, equillibriation or Production MD?
CHARMM-GUI provides you with a series of input files for EM, 
equilibration, and production runs, as well as a README file that tells 
you what to do with them.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] CHARMM GUI membrane builder's assembled output

[Yogesh Sharma]

Greetings,
I used charmm gui's custom Membrane/protein builder to assemble components
for MD simulation. It gave me equillibriated box. I am confused whether I
should equllibriate box again or not? From which step should I start in
Gromac,Energy minimization, equillibriation or Production MD?
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Charmm-Gui output to Gromacs

[Justin Lemkul]

On 5/4/18 5:35 AM, Mark Abraham wrote:

Hi,

Charmm-GUI writes GROMACS files natively, doesn't it?


It does. I haven't run the Glycan Reader directly but it is embedded as 
a component of the Quick MD Simulator, which gives all necessary GROMACS 
input files (coordinates, topology, and .mdp).


-Justin


Mark

On Fri, May 4, 2018 at 10:16 AM Frederic Schneider <
frederic.schnei...@tu-bs.de> wrote:


Hello everyone,

i would like to convert the topology files from the output of the
Charmm-Gui/Glycan Reader(.psf file) to the Gromacs format (.itp, .top).

Is there a preferred script or program to do this task?

Best regards,

Frederic

Frederic Schneider, M.Sc.
TU Braunschweig
Institut für Medizinische und
Pharmazeutische Chemie
Beethovenstraße 55
38106 Braunschweig
Tel.:+49 (0)5 31/ 391 84 51

--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Charmm-Gui output to Gromacs

[Mark Abraham]

Hi,

Charmm-GUI writes GROMACS files natively, doesn't it?

Mark

On Fri, May 4, 2018 at 10:16 AM Frederic Schneider <
frederic.schnei...@tu-bs.de> wrote:

> Hello everyone,
>
> i would like to convert the topology files from the output of the
> Charmm-Gui/Glycan Reader(.psf file) to the Gromacs format (.itp, .top).
>
> Is there a preferred script or program to do this task?
>
> Best regards,
>
> Frederic
>
> Frederic Schneider, M.Sc.
> TU Braunschweig
> Institut für Medizinische und
> Pharmazeutische Chemie
> Beethovenstraße 55
> 38106 Braunschweig
> Tel.:+49 (0)5 31/ 391 84 51
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Charmm-Gui output to Gromacs

[Frederic Schneider]

Hello everyone,

i would like to convert the topology files from the output of the 
Charmm-Gui/Glycan Reader(.psf file) to the Gromacs format (.itp, .top).


Is there a preferred script or program to do this task?

Best regards,

Frederic

Frederic Schneider, M.Sc.
TU Braunschweig
Institut für Medizinische und
Pharmazeutische Chemie
Beethovenstraße 55
38106 Braunschweig
Tel.:+49 (0)5 31/ 391 84 51

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] charmm-gui

[m g]

Dear Justin,Can I use the charmm-gui output file for peptide (.itp file) as an 
input file for GROMACS, and instead of one peptide, I set 4 peptides in the 
bulk of water and near the head groups?In fact , I want to extract manually 
peptide from the final .gro file containing peptide + lipids + ion +water, and 
set four peptides in the bulk of water and near the head groups.Is it possible? 
What is the pathway exactly ? I want to use the same force field for peptide 
and lipid that obtained from CHARMM-GUI.
Would you please help me?thanks,Ganj
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] charmm-gui

[Justin Lemkul]

On 4/4/18 4:49 PM, m g wrote:

Dear Justin, I am using charmm-gui to generate the lipid bilayer according to 
CHARMM36 force field. I embed the peptide in bilayer. Is the file produced for 
peptides, which is based on the CHARMM36, can be used in simulation with 
GROMACS(because I want to used 4 peptide in my bilayer)? Can I extract peptide 
from bilayer and I set four of that in the bilayer again? Can I used the 
CHARMM27  for peptide, and CHARMM36 for bilayer? is it true? Would you please 
help me?


I don't really understand the question. If you're building different 
systems, you can just have CHARMM-GUI build everything rather than 
trying to hack the files.


I also don't recommend using CHARMM22/CMAP for the protein (please note: 
there is no such thing as CHARMM27 for proteins, it's a common 
confusion). The latest CHARMM36 parameters are superior in all regards, 
particularly with the latest CHARMM36m modification for proteins.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] charmm-gui

[m g]

Dear Justin, I am using charmm-gui to generate the lipid bilayer according to 
CHARMM36 force field. I embed the peptide in bilayer. Is the file produced for 
peptides, which is based on the CHARMM36, can be used in simulation with 
GROMACS(because I want to used 4 peptide in my bilayer)? Can I extract peptide 
from bilayer and I set four of that in the bilayer again? Can I used the 
CHARMM27  for peptide, and CHARMM36 for bilayer? is it true? Would you please 
help me?
Thanks,Ganj
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

[gozde ergin]

Ok I will. Thank you very much Justin.
> On 02 Sep 2016, at 16:58, Justin Lemkul  wrote:
> 
> 
> 
> On 9/2/16 10:44 AM, Justin Lemkul wrote:
>> 
>> 
>> On 9/2/16 10:43 AM, gozde ergin wrote:
>>> Ok I understand. I did exactly same thing for another molecule (SDS) and
>>> everything is working without any error.
>>> But I do not know what should I do with cis-pinonic.
>>> 
>> 
>> If you upload a tarball of all the GROMACS files provided by CHARMM-GUI, I 
>> will
>> take a quick look.
>> 
> 
> Contact the CHARMM-GUI developers. The problem is that the parameters 
> specific to the cis-pinonic acid present in lig/lig.prm have not been 
> included when the force field was converted, so only parameters in the ligand 
> that are taken from the parent force field are present.  So their conversion 
> script has a bug.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

[Justin Lemkul]

On 9/2/16 10:44 AM, Justin Lemkul wrote:



On 9/2/16 10:43 AM, gozde ergin wrote:

Ok I understand. I did exactly same thing for another molecule (SDS) and
everything is working without any error.
But I do not know what should I do with cis-pinonic.



If you upload a tarball of all the GROMACS files provided by CHARMM-GUI, I will
take a quick look.



Contact the CHARMM-GUI developers. The problem is that the parameters specific 
to the cis-pinonic acid present in lig/lig.prm have not been included when the 
force field was converted, so only parameters in the ligand that are taken from 
the parent force field are present.  So their conversion script has a bug.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

[Justin Lemkul]

On 9/2/16 10:43 AM, gozde ergin wrote:

Ok I understand. I did exactly same thing for another molecule (SDS) and 
everything is working without any error.
But I do not know what should I do with cis-pinonic.



If you upload a tarball of all the GROMACS files provided by CHARMM-GUI, I will 
take a quick look.


-Justin


On 02 Sep 2016, at 16:40, Justin Lemkul  wrote:



On 9/2/16 10:39 AM, gozde ergin wrote:

Hi Justin,

I try to use the CHARMM-GUI files directly. My purpose is simulating the water 
and ci-pinonic system. Cis-pionic molecules will stay on the water surface and 
I would like to estimate surface tension reduction.

What should I change in CHARMM-GUI files?


Nothing.  That's my point.  When the system is constructed, CHARMM-GUI builds a 
PSF and list of force field parameters that it needs.  This information is then 
converted to GROMACS format.  CHARMM-GUI does an energy evaluation to confirm 
that everything is present.  That's why it's a bit mystifying that GROMACS 
fails; by definition, the system, topology, and force field have already been 
checked for integrity.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.




--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

[gozde ergin]

Ok I understand. I did exactly same thing for another molecule (SDS) and 
everything is working without any error.
But I do not know what should I do with cis-pinonic.

> On 02 Sep 2016, at 16:40, Justin Lemkul  wrote:
> 
> 
> 
> On 9/2/16 10:39 AM, gozde ergin wrote:
>> Hi Justin,
>> 
>> I try to use the CHARMM-GUI files directly. My purpose is simulating the 
>> water and ci-pinonic system. Cis-pionic molecules will stay on the water 
>> surface and I would like to estimate surface tension reduction.
>> 
>> What should I change in CHARMM-GUI files?
> 
> Nothing.  That's my point.  When the system is constructed, CHARMM-GUI builds 
> a PSF and list of force field parameters that it needs.  This information is 
> then converted to GROMACS format.  CHARMM-GUI does an energy evaluation to 
> confirm that everything is present.  That's why it's a bit mystifying that 
> GROMACS fails; by definition, the system, topology, and force field have 
> already been checked for integrity.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

[Justin Lemkul]

On 9/2/16 10:39 AM, gozde ergin wrote:

Hi Justin,

I try to use the CHARMM-GUI files directly. My purpose is simulating the water 
and ci-pinonic system. Cis-pionic molecules will stay on the water surface and 
I would like to estimate surface tension reduction.

What should I change in CHARMM-GUI files?


Nothing.  That's my point.  When the system is constructed, CHARMM-GUI builds a 
PSF and list of force field parameters that it needs.  This information is then 
converted to GROMACS format.  CHARMM-GUI does an energy evaluation to confirm 
that everything is present.  That's why it's a bit mystifying that GROMACS 
fails; by definition, the system, topology, and force field have already been 
checked for integrity.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

[gozde ergin]

Hi Justin,

I try to use the CHARMM-GUI files directly. My purpose is simulating the water 
and ci-pinonic system. Cis-pionic molecules will stay on the water surface and 
I would like to estimate surface tension reduction. 

What should I change in CHARMM-GUI files?
> 
> CHARMM-GUI provides a self-contained force field file that will have 
> everything you need. It is a subset of the full CHARMM force field plus any 
> parameters that are newly introduced by your non-standard molecule.  Are you 
> using only files directly from CHARMM-GUI, without modification, or are you 
> trying to do something else?
> 
> -Justin
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

[Justin Lemkul]

On 9/2/16 10:28 AM, gozde ergin wrote:

Dear all,

I used CHARMM-Gui and prepared the .pdb, .itp and .top file for cis pionic acid.
After that I used genbox command of gromacs and add some water molecules.
When I try to run I get 100 Errors saying :

No default bond types, No default U-B types, No default Proper Dih. types, No 
default Improper Dih. types.

All these errors are related to .itp file. However .itp files seems correct:

Any help would be appreciated. Thanks.




CHARMM-GUI provides a self-contained force field file that will have everything 
you need.  It is a subset of the full CHARMM force field plus any parameters 
that are newly introduced by your non-standard molecule.  Are you using only 
files directly from CHARMM-GUI, without modification, or are you trying to do 
something else?


-Justin


;;
;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7
;;
;; psf2itp_mol.py
;;
;; Correspondance:
;; j712l...@ku.edu or won...@ku.edu
;;
;; GROMACS topology file for LIG
;;


[ moleculetype ]
; name  nrexcl
LIG  3

[ atoms ]
; nrtyperesnr   residu  atomcgnrcharge  mass
 1 CG3C41  1  LIG C2  1 -0.08712.0110   ; qtot 
-0.087
 2 CG3C41  1  LIG C1  2 -0.04612.0110   ; qtot 
-0.133
 3   HGA1  1  LIG H1  3  0.090 1.0080   ; qtot 
-0.043
 4 CG3C41  1  LIG C3  4 -0.03812.0110   ; qtot 
-0.081
 5  CG2O5  1  LIG C8  5  0.38812.0110   ; qtot  
0.307
 6   HGA1  1  LIG H2  6  0.090 1.0080   ; qtot  
0.397
 7  OG2D3  1  LIG O1  7 -0.48115.9994   ; qtot 
-0.084
 8  CG331  1  LIGC10  8 -0.22912.0110   ; qtot 
-0.313
 9   HGA3  1  LIGH14  9  0.090 1.0080   ; qtot 
-0.223
10   HGA3  1  LIGH15 10  0.090 1.0080   ; qtot 
-0.133
11   HGA3  1  LIGH13 11  0.090 1.0080   ; qtot 
-0.043
12 CG3C41  1  LIG C4 12 -0.17812.0110   ; qtot 
-0.221
13   HGA2  1  LIG H4 13  0.090 1.0080   ; qtot 
-0.131
14   HGA2  1  LIG H3 14  0.090 1.0080   ; qtot 
-0.041
15  CG331  1  LIG C6 15 -0.24812.0110   ; qtot 
-0.289
16   HGA3  1  LIGH10 16  0.090 1.0080   ; qtot 
-0.199
17   HGA3  1  LIG H9 17  0.090 1.0080   ; qtot 
-0.109
18   HGA3  1  LIG H8 18  0.090 1.0080   ; qtot 
-0.019
19  CG331  1  LIG C5 19 -0.24812.0110   ; qtot 
-0.267
20   HGA3  1  LIG H6 20  0.090 1.0080   ; qtot 
-0.177
21   HGA3  1  LIG H7 21  0.090 1.0080   ; qtot 
-0.087
22   HGA3  1  LIG H5 22  0.090 1.0080   ; qtot  
0.003
23  CG321  1  LIG C7 23 -0.20712.0110   ; qtot 
-0.204
24  CG2O2  1  LIG C9 24  0.80312.0110   ; qtot  
0.599
25   HGA2  1  LIGH12 25  0.090 1.0080   ; qtot  
0.689
26   HGA2  1  LIGH11 26  0.090 1.0080   ; qtot  
0.779
27  OG2D1  1  LIG O3 27 -0.57615.9994   ; qtot  
0.203
28  OG311  1  LIG O2 28 -0.63215.9994   ; qtot 
-0.429
29   HGP1  1  LIGH16 29  0.429 1.0080   ; qtot  
0.000

[ bonds ]
; aiaj  funct   b0  Kb
1 2 1
1 3 1
112 1
123 1
2 4 1
215 1
219 1
4 5 1
4 6 1
412 1
5 7 1
5 8 1
8 9 1
810 1
811 1
   1213 1
   1214 1
   1516 1
   1517 1
   1518 1
   1920 1
   1921 1
   1922 1
   2324 1
   2325 1
   2326 1
   2427 1
   2428 1
   2829 1

[ pairs ]
; aiaj  funct   c6  c12
1 2 1
1 5 1
1 6 1
112 1
116 1
117 1
118 1
120 1
121 1
122 1
127 1
128 1
2 4 1
2 7 1
2 8 1
213 1
214 1
224 1
225 1
226 1
3 4 1
313 1
314 1
315 1
319 1
324 1
325 1
326 1
4 9 1
410 1
411 1
412 1
416 1
417 1
418 1
420 1
421 1
422 1
423 1
513 1
5

[gmx-users] CHARMM-GUI files give error in Gromacs

[gozde ergin]

Dear all,

I used CHARMM-Gui and prepared the .pdb, .itp and .top file for cis pionic acid.
After that I used genbox command of gromacs and add some water molecules.
When I try to run I get 100 Errors saying : 

No default bond types, No default U-B types, No default Proper Dih. types, No 
default Improper Dih. types.

All these errors are related to .itp file. However .itp files seems correct:

Any help would be appreciated. Thanks.


;;
;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7
;;
;; psf2itp_mol.py
;;
;; Correspondance:
;; j712l...@ku.edu or won...@ku.edu
;;
;; GROMACS topology file for LIG
;;


[ moleculetype ]
; name  nrexcl
LIG  3

[ atoms ]
; nrtyperesnr   residu  atomcgnrcharge  mass
 1 CG3C41  1  LIG C2  1 -0.08712.0110   ; qtot 
-0.087
 2 CG3C41  1  LIG C1  2 -0.04612.0110   ; qtot 
-0.133
 3   HGA1  1  LIG H1  3  0.090 1.0080   ; qtot 
-0.043
 4 CG3C41  1  LIG C3  4 -0.03812.0110   ; qtot 
-0.081
 5  CG2O5  1  LIG C8  5  0.38812.0110   ; qtot  
0.307
 6   HGA1  1  LIG H2  6  0.090 1.0080   ; qtot  
0.397
 7  OG2D3  1  LIG O1  7 -0.48115.9994   ; qtot 
-0.084
 8  CG331  1  LIGC10  8 -0.22912.0110   ; qtot 
-0.313
 9   HGA3  1  LIGH14  9  0.090 1.0080   ; qtot 
-0.223
10   HGA3  1  LIGH15 10  0.090 1.0080   ; qtot 
-0.133
11   HGA3  1  LIGH13 11  0.090 1.0080   ; qtot 
-0.043
12 CG3C41  1  LIG C4 12 -0.17812.0110   ; qtot 
-0.221
13   HGA2  1  LIG H4 13  0.090 1.0080   ; qtot 
-0.131
14   HGA2  1  LIG H3 14  0.090 1.0080   ; qtot 
-0.041
15  CG331  1  LIG C6 15 -0.24812.0110   ; qtot 
-0.289
16   HGA3  1  LIGH10 16  0.090 1.0080   ; qtot 
-0.199
17   HGA3  1  LIG H9 17  0.090 1.0080   ; qtot 
-0.109
18   HGA3  1  LIG H8 18  0.090 1.0080   ; qtot 
-0.019
19  CG331  1  LIG C5 19 -0.24812.0110   ; qtot 
-0.267
20   HGA3  1  LIG H6 20  0.090 1.0080   ; qtot 
-0.177
21   HGA3  1  LIG H7 21  0.090 1.0080   ; qtot 
-0.087
22   HGA3  1  LIG H5 22  0.090 1.0080   ; qtot  
0.003
23  CG321  1  LIG C7 23 -0.20712.0110   ; qtot 
-0.204
24  CG2O2  1  LIG C9 24  0.80312.0110   ; qtot  
0.599
25   HGA2  1  LIGH12 25  0.090 1.0080   ; qtot  
0.689
26   HGA2  1  LIGH11 26  0.090 1.0080   ; qtot  
0.779
27  OG2D1  1  LIG O3 27 -0.57615.9994   ; qtot  
0.203
28  OG311  1  LIG O2 28 -0.63215.9994   ; qtot 
-0.429
29   HGP1  1  LIGH16 29  0.429 1.0080   ; qtot  
0.000

[ bonds ]
; aiaj  funct   b0  Kb
1 2 1
1 3 1
112 1
123 1
2 4 1
215 1
219 1
4 5 1
4 6 1
412 1
5 7 1
5 8 1
8 9 1
810 1
811 1
   1213 1
   1214 1
   1516 1
   1517 1
   1518 1
   1920 1
   1921 1
   1922 1
   2324 1
   2325 1
   2326 1
   2427 1
   2428 1
   2829 1

[ pairs ]
; aiaj  funct   c6  c12
1 2 1 
1 5 1 
1 6 1 
112 1 
116 1 
117 1 
118 1 
120 1 
121 1 
122 1 
127 1 
128 1 
2 4 1 
2 7 1 
2 8 1 
213 1 
214 1 
224 1 
225 1 
226 1 
3 4 1 
313 1 
314 1 
315 1 
319 1 
324 1 
325 1 
326 1 
4 9 1 
410 1 
411 1 
412 1 
416 1 
417 1 
418 1 
420 1 
421 1 
422 1 
423 1 
513 1 
514 1 
515 1 
519 1 
6 7 1 
6 8 1 
613 1 
614 1 
615 1 
619 1 
7 9 1 
710 1 
711 1 
712 1 
812 1 
   1215 1 
   1219 1 
   1224 1 
   1225 1 
   1226 

Re: [gmx-users] CHARMM-GUI Membrane building problems

[Björn Sommer]

Message: 5
Date: Fri, 6 May 2016 06:51:55 -0400
From: Justin Lemkul<jalem...@vt.edu>
To:gmx-us...@gromacs.org
Subject: Re: [gmx-users] CHARMM-GUI Membrane building problems
Message-ID:<7d29cbd8-6111-3a02-eddf-9f5e77d22...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 5/5/16 11:41 AM, John Smith wrote:

Hello,

I am resending this message from my Gmail account, as it appears that
messages sent from my Yahoo account are going to spam. Apologies if you
have already seen this.

I am trying to build a simple DOPC-DPPC-Cholesterol bilayer with
CHARMM-GUI. The process seems to be fairly straightforward. Unfortunately,
there are problems with the resulting configuration of the membrane. After
running the equilibration scripts provided as part of the Charmm-GUI output
download, with the default MDP files provided, I see that several of the
lipids are resting in horizontal positions on the "top" of the bilayer
(e.g. a DOPC molecule with chains pointing sideways instead of into the
bilayer). So, I tried more strongly position-restraining the head-groups of
all three molecule types in z, and re-ran all the equilibrations from the
beginning. Unfortunately, I still see a couple DOPC and Cholesterol
molecules horizontally on the top of the bilayer. Any suggestions as to why
this might be, and how one might prevent it? I could weakly position
restrain the ends of the lipid chains in z as well, but I am not sure
whether this might have unwanted side effects during the equilibration.


Are the starting coordinates sane?  How quickly does the problem occur?  Any
visual clues as to what's going on from watching the trajectories?  I have never
seen such a thing happen, and the force required for such a displacement would
be rather large.

-Justin


Sincerely,
John



Hi John, might there be a problem with the box size? Maybe CHARMM-GUI 
defined the box size in the wrong and was not able to cope with that? 
Maybe it is possible to extend the vertical size of the box a little bit.


Anyway, first you should try what Justin proposed, use e.g. VMD and have a look 
at the starting configuration and load the tragjectory in case the lipids are 
not inversely positioned right from the start. In the worst case, the packing 
algorithm of CHARMM-GUI does not work correctly here. Then you could use our Cm 
MembraneEditor (with Java GUI) or PackMol (with Scripting) to generate the 
membrane.

Have fun! Bjorn
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CHARMM-GUI Membrane building problems

[Justin Lemkul]

On 5/5/16 11:41 AM, John Smith wrote:

Hello,

I am resending this message from my Gmail account, as it appears that
messages sent from my Yahoo account are going to spam. Apologies if you
have already seen this.

I am trying to build a simple DOPC-DPPC-Cholesterol bilayer with
CHARMM-GUI. The process seems to be fairly straightforward. Unfortunately,
there are problems with the resulting configuration of the membrane. After
running the equilibration scripts provided as part of the Charmm-GUI output
download, with the default MDP files provided, I see that several of the
lipids are resting in horizontal positions on the "top" of the bilayer
(e.g. a DOPC molecule with chains pointing sideways instead of into the
bilayer). So, I tried more strongly position-restraining the head-groups of
all three molecule types in z, and re-ran all the equilibrations from the
beginning. Unfortunately, I still see a couple DOPC and Cholesterol
molecules horizontally on the top of the bilayer. Any suggestions as to why
this might be, and how one might prevent it? I could weakly position
restrain the ends of the lipid chains in z as well, but I am not sure
whether this might have unwanted side effects during the equilibration.



Are the starting coordinates sane?  How quickly does the problem occur?  Any 
visual clues as to what's going on from watching the trajectories?  I have never 
seen such a thing happen, and the force required for such a displacement would 
be rather large.


-Justin


Sincerely,
John



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] CHARMM-GUI Membrane building problems

[John Smith]

Hello,

I am resending this message from my Gmail account, as it appears that
messages sent from my Yahoo account are going to spam. Apologies if you
have already seen this.

I am trying to build a simple DOPC-DPPC-Cholesterol bilayer with
CHARMM-GUI. The process seems to be fairly straightforward. Unfortunately,
there are problems with the resulting configuration of the membrane. After
running the equilibration scripts provided as part of the Charmm-GUI output
download, with the default MDP files provided, I see that several of the
lipids are resting in horizontal positions on the "top" of the bilayer
(e.g. a DOPC molecule with chains pointing sideways instead of into the
bilayer). So, I tried more strongly position-restraining the head-groups of
all three molecule types in z, and re-ran all the equilibrations from the
beginning. Unfortunately, I still see a couple DOPC and Cholesterol
molecules horizontally on the top of the bilayer. Any suggestions as to why
this might be, and how one might prevent it? I could weakly position
restrain the ends of the lipid chains in z as well, but I am not sure
whether this might have unwanted side effects during the equilibration.

Sincerely,
John
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] CHARMM-GUI Membrane building problems

[John Smith]

Hello All,
I am trying to build a simple DOPC-DPPC-Cholesterol bilayer with CHARMM-GUI. 
The process seems to be fairly straightforward. Unfortunately, there are 
problems with the resulting configuration of the membrane. After running the 
equilibration scripts provided as part of the Charmm-GUI output download, with 
the default MDP files provided, I see that several of the lipids are resting in 
horizontal positions on the "top" of the bilayer (e.g. a DOPC molecule with 
chains pointing sideways instead of into the bilayer). So, I tried more 
strongly position-restraining the head-groups of all three molecule types in z, 
and re-ran all the equilibrations from the beginning. Unfortunately, I still 
see a couple Cholesterol molecules horizontally on the top of the bilayer. Any 
suggestions as to why this might be, and how one might prevent it? I could 
weakly position restrain the ends of the lipid chains in z as well, but I am 
not sure whether this might have unwanted side effects.
Sincerely,John
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Charmm gui error when making topology

[Nikhil Maroli]

Dear all,
im trying to make topology for few ligands,(CHARMM ff)when  i try to run it
end with error

i made unique name for all atoms using VMD-molfacature tool

and used Discovery studio,open babel to convert to mol2 file for uploading
to charmm-gui
im getting following error


awk: cmd. line:1: fatal: cannot open file `LIG.mol2' for reading (No
such file or directory)
Cannot open file LIG.mol2 to read in rmol2(), exit


or

readmol2 warning: skipped empty mol2 file



i hope someone can help me out here



-- 
Ragards,
Nikhil Maroli
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Charmm gui error when making topology

[Justin Lemkul]

On 12/30/15 9:21 AM, Nikhil Maroli wrote:

Dear all,
im trying to make topology for few ligands,(CHARMM ff)when  i try to run it
end with error

i made unique name for all atoms using VMD-molfacature tool

and used Discovery studio,open babel to convert to mol2 file for uploading
to charmm-gui
im getting following error


awk: cmd. line:1: fatal: cannot open file `LIG.mol2' for reading (No
such file or directory)
Cannot open file LIG.mol2 to read in rmol2(), exit


or

readmol2 warning: skipped empty mol2 file



i hope someone can help me out here



Contact the CHARMM-GUI team; this is not a GROMACS problem.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] CHARMM-GUI: new features for GROMACS

[Justin Lemkul]

Hi All,

I am pleased to announce that the CHARMM-GUI team has extended the capabilities 
of CHARMM-GUI (www.charmm-gui.org) to provide GROMACS topologies, .mdp files, 
and run scripts as part of the standard output of CHARMM-GUI.  That is, one can 
now assemble a system (even heterogeneous membranes with embedded proteins) 
using CHARMM-GUI and immediately proceed to minimization and dynamics - no more 
tedious separation of water or other components to input into pdb2gmx! 
Everything you will need is in the gromacs subdirectory of the downloaded 
tarball.  The input files assume you are using version 5.0 or higher.


The .mdp files have been compared against the CHARMM program and have been found 
to yield equivalent forces, so you can be assured that these are the correct 
settings to be used with the CHARMM36 force field.  The equilibration protocol 
for membrane systems (please see the README file in the downloaded tarball) has 
been highly optimized to gently relax the system for maximum stability.


We hope that these new features will streamline your workflows and make the 
construction of complex systems even easier.  If there are any questions or 
comments, please send them to the CHARMM-GUI team via the email link at 
www.charmm-gui.org


Happy simulating!

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.