[gmx-users] Re:Re: How to get sufactant.gro, sufactant.top, (Mark Abraham)

gromacs ptf1242 at 163.com
Wed Jan 5 07:37:34 CET 2011 

Sorry, i write wrong.
 
Someone said that we cannot get sufactant.gro and sufactant.top through pdb2gmx()  sufactant.pdb. Because grompp  .pdb could mainly use for macro-biology big moleculars, which means some proteins etc.
 
 So that means we could not get correct  .gro, .top small molecules such as inorganic or small organic molecules (such as ethanol) by using pdb2max command.
 
Maybe we could get get sufactant.gro, sufactant.top through the following?SwissParam (for CHARMM forcefield),PRODRG (for ffgmx/GROMOS96 43A1),Automated Topology Builder (for GROMOS96 53A6), MKTOP (for OPLS/AA)
?
But how can we get surfactant such as SDS .gro?





At 2011-01-04 16:19:05，gmx-users-request at gromacs.org wrote:

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>   1. Re: Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study
>      (wibke.sudholt at cloudbroker.com)
>   2. Email bounce message (Mark Abraham)
>   3. g_mindist (Ramachandran G)
>   4. Re: g_mindist (Justin A. Lemkul)
>   5. Re: The sum of the O-H distancesof the backbone hydrogen
>      bonds ROH (sreelakshmi ramesh)
>   6. How to get sufactant.gro, sufactant.top, (gromacs)
>   7. Re: How to get sufactant.gro, sufactant.top, (Mark Abraham)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: 4 Jan 2011 01:23:06 +0100
>From: wibke.sudholt at cloudbroker.com
>Subject: Re: Re: [gmx-users] Trifluoroethanol-Ethanol mixtures study
>To: gmx-users at gromacs.org
>Message-ID: <20110104002306.1761.qmail at server12.hostfactory.ch>
>Content-Type: text/plain; charset="UTF-8"
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>Dear Email Sender,
>
>Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, January 10, 2011.
>
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>------------------------------
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>Message: 2
>Date: Tue, 04 Jan 2011 11:27:29 +1100
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: [gmx-users] Email bounce message
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4D226971.8000808 at anu.edu.au>
>Content-Type: text/plain; charset=UTF-8; format=flowed
>
>On 4/01/2011 11:23 AM, wibke.sudholt at cloudbroker.com wrote:
>> Dear Email Sender,
>>
>> Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, January 10, 2011.
>>
>> For all questions about CloudBroker, please contact the company under info at cloudbroker.com. In case you have any issues with the CloudBroker Platform, please send an email to our helpdesk at platform at cloudbroker.com. If you need to talk to me in person for urgent or important issues, please call my mobile phone number.
>
>Can we unsubscribe this email address please? I've now had a slew of 
>bounces from them.
>
>Thanks,
>
>Mark
>
>
>------------------------------
>
>Message: 3
>Date: Mon, 3 Jan 2011 17:20:23 -0800
>From: Ramachandran G <gtrama at gmail.com>
>Subject: [gmx-users] g_mindist
>To: gmx-users at gromacs.org
>Message-ID:
>	<AANLkTiktntrig9cT1zpQ3uFUPfOiY2pfAEbTA8B+thb4 at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi Gromacs users,
>    I used g_mindist to calculate the minimum distance between a residue and
>a group of water molecules.
>Since distance is a length between two points in space, for the program
>considers the bunch of water molecules(15 number)
>what specific point does the group consider ? Thank you.
>
>Yours sincerely,
>Rama
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>Message: 4
>Date: Mon, 03 Jan 2011 20:29:02 -0500
>From: "Justin A. Lemkul" <jalemkul at vt.edu>
>Subject: Re: [gmx-users] g_mindist
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <4D2277DE.6080008 at vt.edu>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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>
>
>Ramachandran G wrote:
>> Hi Gromacs users,
>>     I used g_mindist to calculate the minimum distance between a residue 
>> and a group of water molecules.
>> Since distance is a length between two points in space, for the program 
>> considers the bunch of water molecules(15 number)
>> what specific point does the group consider ? Thank you.
>> 
>
>The distance measured is that between the two closest atoms, whichever those may 
>be.  Read the first few sentences of g_mindist -h.
>
>-Justin
>
>> Yours sincerely,
>> Rama
>> 
>> 
>> 
>
>-- 
>========================================
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>MILES-IGERT Trainee
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
>
>------------------------------
>
>Message: 5
>Date: Tue, 4 Jan 2011 11:59:53 +0530
>From: sreelakshmi ramesh <sree.lakshmi at research.iiit.ac.in>
>Subject: Re: [gmx-users] The sum of the O-H distancesof the backbone
>	hydrogen	bonds ROH
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID:
>	<AANLkTikw-M-NCBpnkAj8RxnrVjrDEzYPsNCfmMbiHV0V at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Thanks a lot for your reply..
>
>On Mon, Jan 3, 2011 at 6:07 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
>> On 2/01/2011 2:18 PM, sreelakshmi ramesh wrote:
>>
>>> Dear all,
>>>             I have a protein in water and i have simulated it for few
>>> nanoseconds and i now i wanted to monitor the  The sum of the O-H distances
>>> (in Å) of the backbone
>>> hydrogen bonds ROH:i dono how to extract the value from the trajectory
>>> file.Any siuggestion please.Thanks in advance
>>>
>>
>> Look in section 7.4 of the manual for a suitable tool for extracting the
>> raw distances. You'll need some other non-GROMACS tool to add them up.
>>
>> Mark
>> --
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>------------------------------
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>Message: 6
>Date: Tue, 4 Jan 2011 15:45:57 +0800 (CST)
>From: gromacs <ptf1242 at 163.com>
>Subject: [gmx-users] How to get sufactant.gro, sufactant.top,
>To: gmx-users at gromacs.org
>Message-ID: <7bda4963.110c4.12d4ffd516f.Coremail.ptf1242 at 163.com>
>Content-Type: text/plain; charset="gbk"
>
>Hi expert,
> 
>I'd like to add sufactant to water. That means i should first get the sufactant.gro, and sufactant.top.
> 
>Someone said that we cannot get sufactant.gro and sufactant.top through grompp ()  sufactant.pdb. Because grompp  .pdb could mainly use for macro-biology big moleculars, which means some proteins etc.
>So that means we could not get correct  .gro, .top small molecules such as inorganic or small organic molecules (such asethanol).
> 
>So how can we get the sufactant.gro, sufactant.top? and which force field should we choose for ordinary simulation? I know we often use ffoplass force field for solution.
> 
>Tiefeng
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>------------------------------
>
>Message: 7
>Date: Tue, 04 Jan 2011 19:18:10 +1100
>From: Mark Abraham <mark.abraham at anu.edu.au>
>Subject: Re: [gmx-users] How to get sufactant.gro, sufactant.top,
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <7690a1161265.4d237272 at anu.edu.au>
>Content-Type: text/plain; charset="iso-8859-1"
>
>On 01/04/11, gromacs  <ptf1242 at 163.com> wrote:
>> Hi expert,
>> 
>>  
>> 
>> I'd like to add sufactant to water. That means i should first get the sufactant.gro, and sufactant.top.
>> 
>> 
>
>No, you need a coordinate file for the starting point for your GROMACS work, and the pieces to combine into a .top. That might mean a coordinate file of all your surfactant molecules and matching .top file that you then solvate with genbox. Or you might want to use genconf to replicate some existing coordinate file somehow. Or you might have your starting point already and need to match a .top to it.
> 
>
>> 
>> Someone said that we cannot get sufactant.gro and sufactant.top through grompp ()  sufactant.pdb. Because grompp  .pdb could mainly use for macro-biology big moleculars, which means some proteins etc.
>> 
>> 
>
>Well they (or your account of them) is wrong on what might be several points. Someone needs to understand GROMACS workflows better - perhaps by doing some tutorial material and/or reading http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>
>
>> 
>> 
>> So that means we could not get correct  .gro, .top small molecules such as inorganic or small organic molecules (such as ethanol).
>> 
>>  
>> 
>> So how can we get the sufactant.gro, sufactant.top?
>> 
>> 
>
>That varies widely with what raw materials exist and what the objective is.
>
>
>>  and which force field should we choose for ordinary simulation? I know we often use ffoplass force field for solution.
>> 
>> 
>
>That's your homework, I'm afraid. See above link.
>
>Mark
>
>
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