Thank you
Em 25/09/2015 5:44 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se
escreveu:
Send gromacs.org_gmx-users mailing list submissions to
gromacs.org_gmx-users@maillist.sys.kth.se
To subscribe or unsubscribe via the World Wide Web, visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or, via email, send a message with subject or body 'help' to
gromacs.org_gmx-users-requ...@maillist.sys.kth.se
You can reach the person managing the list at
gromacs.org_gmx-users-ow...@maillist.sys.kth.se
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gromacs.org_gmx-users digest..."
Today's Topics:
1. Gromacs says that may GeForce 9800gt is incompatible any
help? (Juliano Braz Carregal)
2. Re: Gromacs says that may GeForce 9800gt is incompatible any
help? (Repic Matej)
3. Re: GROMACS with AMBER heme parameters (Ebert Maximilian)
4. Re: GROMACS with AMBER heme parameters (Justin Lemkul)
5. Re: GROMACS with AMBER heme parameters (Ebert Maximilian)
6. Re: GROMACS with AMBER heme parameters (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Fri, 25 Sep 2015 15:46:29 -0300
From: Juliano Braz Carregal <julianocarre...@hotmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Gromacs says that may GeForce 9800gt is
incompatible any help?
Message-ID: <snt406-eas4017586f92e165604307495b8...@phx.gbl>
Content-Type: text/plain; charset="us-ascii"
An HTML attachment was scrubbed...
URL:
<http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20150925/fcc6225b/attachment-0001.html>
------------------------------
Message: 2
Date: Fri, 25 Sep 2015 19:15:43 +0000
From: Repic Matej <matej.re...@epfl.ch>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Gromacs says that may GeForce 9800gt is
incompatible any help?
Message-ID: <d22b692a.12714%matej.re...@epfl.ch>
Content-Type: text/plain; charset="Windows-1252"
Unfortunately, it is incompatible. 9800GT has compute capability 1.1, but
gromacs needs 2.0 or higher. The oldest compatible cards are GTX 4xx series
from 2010, but 9800GT is from 2008.
Best,
------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique F?d?rale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ? LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------
From:
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>>
on behalf of Juliano Braz Carregal
<julianocarre...@hotmail.com<mailto:julianocarre...@hotmail.com>>
Reply-To: "gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>"
<gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>>
Date: Friday, September 25, 2015 at 20:46
To:
"gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@maillist.sys.kth.se>"
<gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@maillist.sys.kth.se>>
Subject: [gmx-users] Gromacs says that may GeForce 9800gt is incompatible
any help?
Gromacs 5 says that may GeForce 9800gt is incompatible any help?
------------------------------
Message: 3
Date: Fri, 25 Sep 2015 20:22:54 +0000
From: Ebert Maximilian <m.eb...@umontreal.ca>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] GROMACS with AMBER heme parameters
Message-ID: <5ef0a589-8604-438c-90ed-55ecb9fc2...@umontreal.ca>
Content-Type: text/plain; charset="us-ascii"
Since the heme definition in AMBER uses GAFF atom types how do I get the
GAFF FF to work in GROMACS? I would need all the bonded and non bonded
definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
Max
> On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
>
> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
>> Hi there,
>>
>> I am trying to simulate a heme containing protein. I found AMBER heme
>> parameters in the mol2 and frcmod file format. I know that I can
generate
>> .itp files containing the parameters, which I can later add to my .top
file.
>> However, it would be much easier to use pdb2gmx directly without
stripping
>> the heme and the cysteine binding the heme and later manually add it
again. I
>> added the cysteine to the standard amber force field. However, before
adding
>> the heme manually I wanted to know if there is a way to load an itp file
>> while executing pdb2gmx?
>>
>
> pdb2gmx does not need .itp information. grompp does. Add the parameters
to ffbonded.itp or ffnonbonded.itp as needed.
>
>> How would you add the information from the cysteine in mol2 format and
the
>> heme in mol2/frcmod format to amber in gromacs?
>>
>
> Charges and connectivity go in the .rtp entry. Heme ligation by His and
Cys is already supported via specbond.dat.
>
> -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.
------------------------------
Message: 4
Date: Fri, 25 Sep 2015 16:25:20 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GROMACS with AMBER heme parameters
Message-ID: <5605adb0.4040...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 9/25/15 4:22 PM, Ebert Maximilian wrote:
> Since the heme definition in AMBER uses GAFF atom types how do I get the
GAFF FF to work in GROMACS? I would need all the bonded and non bonded
definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
>
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
> Max
>
>> On Sep 25, 2015, at 1:36 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>
>> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
>>> Hi there,
>>>
>>> I am trying to simulate a heme containing protein. I found AMBER heme
>>> parameters in the mol2 and frcmod file format. I know that I can
generate
>>> .itp files containing the parameters, which I can later add to my .top
file.
>>> However, it would be much easier to use pdb2gmx directly without
stripping
>>> the heme and the cysteine binding the heme and later manually add it
again. I
>>> added the cysteine to the standard amber force field. However, before
adding
>>> the heme manually I wanted to know if there is a way to load an itp
file
>>> while executing pdb2gmx?
>>>
>>
>> pdb2gmx does not need .itp information. grompp does. Add the
parameters to ffbonded.itp or ffnonbonded.itp as needed.
>>
>>> How would you add the information from the cysteine in mol2 format and
the
>>> heme in mol2/frcmod format to amber in gromacs?
>>>
>>
>> Charges and connectivity go in the .rtp entry. Heme ligation by His and
Cys is already supported via specbond.dat.
>>
>> -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
==================================================
------------------------------
Message: 5
Date: Fri, 25 Sep 2015 20:40:19 +0000
From: Ebert Maximilian <m.eb...@umontreal.ca>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] GROMACS with AMBER heme parameters
Message-ID: <911260f5-ac7d-4111-bfc6-4c8c97923...@umontreal.ca>
Content-Type: text/plain; charset="us-ascii"
I read that and this is the way I added the cysteine to AMBER which connects
to the heme. Now I am adding the heme but the FF definition for bonds,
angles, etc are all in lower case for the GAFF FF. From you answer I guess I
need to add these lower case atom types and the bonds, angles, etc
definition from the GAFF FF to the AMBER FF manually.
Not much fun but I will share the work here in the end. Maybe this will help
people who want to simulate heme containing proteins in GROMACS and
AMBER99SB-ILDN.
Have a good weekend,
Max
On Sep 25, 2015, at 4:25 PM, Justin Lemkul
<jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote:
On 9/25/15 4:22 PM, Ebert Maximilian wrote:
Since the heme definition in AMBER uses GAFF atom types how do I get the
GAFF FF to work in GROMACS? I would need all the bonded and non bonded
definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
Max
On Sep 25, 2015, at 1:36 PM, Justin Lemkul
<jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote:
On 9/25/15 1:32 PM, Ebert Maximilian wrote:
Hi there,
I am trying to simulate a heme containing protein. I found AMBER heme
parameters in the mol2 and frcmod file format. I know that I can generate
.itp files containing the parameters, which I can later add to my .top file.
However, it would be much easier to use pdb2gmx directly without stripping
the heme and the cysteine binding the heme and later manually add it again.
I
added the cysteine to the standard amber force field. However, before adding
the heme manually I wanted to know if there is a way to load an itp file
while executing pdb2gmx?
pdb2gmx does not need .itp information. grompp does. Add the parameters to
ffbonded.itp or ffnonbonded.itp as needed.
How would you add the information from the cysteine in mol2 format and the
heme in mol2/frcmod format to amber in gromacs?
Charges and connectivity go in the .rtp entry. Heme ligation by His and Cys
is already supported via specbond.dat.
-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<mailto: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<mailto: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<mailto:gmx-users-requ...@gromacs.org>.
------------------------------
Message: 6
Date: Fri, 25 Sep 2015 16:43:32 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GROMACS with AMBER heme parameters
Message-ID: <5605b1f4.4050...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 9/25/15 4:40 PM, Ebert Maximilian wrote:
> I read that and this is the way I added the cysteine to AMBER which
connects to the heme. Now I am adding the heme but the FF definition for
bonds, angles, etc are all in lower case for the GAFF FF. From you answer I
guess I need to add these lower case atom types and the bonds, angles, etc
definition from the GAFF FF to the AMBER FF manually.
>
Indeed, which is what steps 3 and 4 tell you. Adding a residue is simple,
but
if that residue involves modifications to the force field, then there is
more
work to be done.
-Justin
> Not much fun but I will share the work here in the end. Maybe this will
help people who want to simulate heme containing proteins in GROMACS and
AMBER99SB-ILDN.
>
> Have a good weekend,
> Max
>
>
> On Sep 25, 2015, at 4:25 PM, Justin Lemkul
<jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote:
>
>
>
> On 9/25/15 4:22 PM, Ebert Maximilian wrote:
> Since the heme definition in AMBER uses GAFF atom types how do I get the
GAFF FF to work in GROMACS? I would need all the bonded and non bonded
definitions of GAFF for the heme in der AMBER FF port in GROMACS right?
>
>
>
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> -Justin
>
> Max
>
> On Sep 25, 2015, at 1:36 PM, Justin Lemkul
<jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote:
>
>
>
> On 9/25/15 1:32 PM, Ebert Maximilian wrote:
> Hi there,
>
> I am trying to simulate a heme containing protein. I found AMBER heme
> parameters in the mol2 and frcmod file format. I know that I can generate
> .itp files containing the parameters, which I can later add to my .top
file.
> However, it would be much easier to use pdb2gmx directly without
stripping
> the heme and the cysteine binding the heme and later manually add it
again. I
> added the cysteine to the standard amber force field. However, before
adding
> the heme manually I wanted to know if there is a way to load an itp file
> while executing pdb2gmx?
>
>
> pdb2gmx does not need .itp information. grompp does. Add the parameters
to ffbonded.itp or ffnonbonded.itp as needed.
>
> How would you add the information from the cysteine in mol2 format and
the
> heme in mol2/frcmod format to amber in gromacs?
>
>
> Charges and connectivity go in the .rtp entry. Heme ligation by His and
Cys is already supported via specbond.dat.
>
> -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<mailto: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<mailto: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<mailto: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.
End of gromacs.org_gmx-users Digest, Vol 137, Issue 137
*******************************************************
