Re: [gmx-users] question about all atoms lipid molecule structure and force field
Amit Choubey wrote:
Thank you,
Is it really necessary for me to use Charmm FF for all atom calculations
on lipids?
You can use whatever model you want, provided it's valid. Just so happens that
most people who use all-atom models of lipids use CHARMM.
The reason I am asking this is because it will require me to create
gromacs compatible FF files of the Charmm FF . I did find two perl
scripts which can do probably handle that but i am wondering if the
compatible FF are already up on gromacs website somewhere.
No one ever said life was easy :) CHARMM support is under development, you can
get the source via the git repositories, but I don't know its current status.
-Justin
amit
2009/10/14 LuLanyuan mailto:lulany...@msn.com>>
Hi,
You can find some configurations here:
http://persweb.wabash.edu/facstaff/fellers/
And I think you can use Charmm FF.
Lanyuan
Date: Wed, 14 Oct 2009 11:29:26 -0700
From: kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Subject: [gmx-users] question about all atoms lipid molecule
structure and force field
Dear all,
I have been trying to search for an all atom DPPC sructure
(including the missing Hydrogens of long chain hydrocarbons) and
then do an all atoms md simulation on it. I havent yet found any
such structure or any force field that could be used for it on the
internet. Is anybody familiar with any such work ?
Is there any all atom model for hydrocarbons which is incorporated
in Gromacs? I am not 100 % sure about it.
I want to do this to parametrize another force field which
essentially uses all atom model.
Thank you,
Amit
Messenger保护盾2.0，更安全可靠的Messenger聊天！ 现在就下载！
<http://im.live.cn/safe/>
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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Re: [gmx-users] question about all atoms lipid molecule structure and force field
Thank you, Is it really necessary for me to use Charmm FF for all atom calculations on lipids? The reason I am asking this is because it will require me to create gromacs compatible FF files of the Charmm FF . I did find two perl scripts which can do probably handle that but i am wondering if the compatible FF are already up on gromacs website somewhere. amit 2009/10/14 LuLanyuan > Hi, > You can find some configurations here: > http://persweb.wabash.edu/facstaff/fellers/ > And I think you can use Charmm FF. > Lanyuan > > -- > Date: Wed, 14 Oct 2009 11:29:26 -0700 > From: kgp.a...@gmail.com > To: gmx-users@gromacs.org > Subject: [gmx-users] question about all atoms lipid molecule structure and > force field > > > Dear all, > I have been trying to search for an all atom DPPC sructure (including the > missing Hydrogens of long chain hydrocarbons) and then do an all atoms md > simulation on it. I havent yet found any such structure or any force field > that could be used for it on the internet. Is anybody familiar with any such > work ? > > Is there any all atom model for hydrocarbons which is incorporated in > Gromacs? I am not 100 % sure about it. > > I want to do this to parametrize another force field which essentially uses > all atom model. > > Thank you, > Amit > > -- > Messenger保护盾2.0，更安全可靠的Messenger聊天！ 现在就下载！ <http://im.live.cn/safe/> > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
RE: [gmx-users] question about all atoms lipid molecule structure and force field
Hi, You can find some configurations here: http://persweb.wabash.edu/facstaff/fellers/ And I think you can use Charmm FF. Lanyuan Date: Wed, 14 Oct 2009 11:29:26 -0700 From: kgp.a...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] question about all atoms lipid molecule structure and force field Dear all, I have been trying to search for an all atom DPPC sructure (including the missing Hydrogens of long chain hydrocarbons) and then do an all atoms md simulation on it. I havent yet found any such structure or any force field that could be used for it on the internet. Is anybody familiar with any such work ? Is there any all atom model for hydrocarbons which is incorporated in Gromacs? I am not 100 % sure about it. I want to do this to parametrize another force field which essentially uses all atom model. Thank you,Amit _ MSN十周年庆典，查看MSN注册时间，赢取神秘大奖 http://10.msn.com.cn___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] question about all atoms lipid molecule structure and force field
Dear all, I have been trying to search for an all atom DPPC sructure (including the missing Hydrogens of long chain hydrocarbons) and then do an all atoms md simulation on it. I havent yet found any such structure or any force field that could be used for it on the internet. Is anybody familiar with any such work ? Is there any all atom model for hydrocarbons which is incorporated in Gromacs? I am not 100 % sure about it. I want to do this to parametrize another force field which essentially uses all atom model. Thank you, Amit ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
