[gmx-users] implicit solvent
aixintiankong
aixintiankong at 126.com
Sat Mar 2 14:30:30 CET 2013
Dear,
there are three waters in active site of receptor,mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system.
In order to avoid the three waters exchange with the solvent waters, can i do the ligand-receptor in the implicit solvent. i will prepare two diffrent recepor mode. The one is not water in active site and the other retain waters in the active site. my ideal is good or not?
At 2013-03-02 21:21:38,gmx-users-request at gromacs.org wrote:
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>Today's Topics:
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> 1. Fw:some waters in active site of receptor (aixintiankong)
> 2. Re: removing number of sol (gromacs query)
> 3. Semiisotropic pressure coupling problem (congchen)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Sat, 2 Mar 2013 18:59:27 +0800 (CST)
>From: aixintiankong <aixintiankong at 126.com>
>Subject: [gmx-users] Fw:some waters in active site of receptor
>To: gmx-users at gromacs.org
>Message-ID:
> <625c04ca.1a6bf.13d2ac1a871.Coremail.aixintiankong at 126.com>
>Content-Type: text/plain; charset=GBK
>
>Dear,
> there are three waters in active site of receptor,mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system.
> In order to avoid the three waters exchange with the solvent waters, can i do the ligand-receptor in the implicit solvent. i will prepare two diffrent recepor mode. The one is not water in active site and the other retain waters in the active site. my ideal is good or not?
>
>
>
>
>
>
>
>
>
>-------- Forwarding messages --------
>From: aixintiankong <aixintiankong at 126.com>
>Date: 2013-02-16 23:54:51
>To: gmx-users at gromacs.org
>Subject: some waters in active site of receptor
>
>Dear,
> there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system.
> In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models of those. when i use the genbox program to add solvent to my system, i find there are many other waters being added to the active site and i think the waters which are added by genbox program maybe replace the initial three waters and then i can't study the waters in active site.
> please hlpe me and then tell me how to do it
>Thank you very much!
>
>
>
>
>
>
>
>------------------------------
>
>Message: 2
>Date: Sat, 2 Mar 2013 15:01:25 +0200
>From: gromacs query <gromacsquery at gmail.com>
>Subject: Re: [gmx-users] removing number of sol
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID:
> <CAPe3FJD4s+Y9KZUPpT_FNRLdUCOpdH-WJS=JmRDgRzSFthqrCg at mail.gmail.com>
>Content-Type: text/plain; charset=ISO-8859-1
>
>Dear Erik,
>
>I am new to Gromacs and used AMBER before, and I am exploring various
>options in GROMACS too. Surely I will look in to g_select. Also as I was
>using sed, one should include an extra space (using vi) in gro file just
>before residue number and then can use sed to remove like this: sed -e '/
>35SOL/d' -e '/ 36SOL/d' -e '/ 38SOL/d' -e '/ 39SOL/d' old.gro > new2.gro
>
>But please note I included an extra space / 35SOL/d (instead of /35SOL/d)
>by this sed will remove 35SOL not 135SOL.
>
>regards,
>
>
>On Fri, Mar 1, 2013 at 5:27 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
>
>> Hi,
>>
>> Then the problem lies in automating what molecules are to be removed,
>> right? Try g_select or look into trjorder.
>>
>> Erik
>>
>>
>> On Mar 1, 2013, at 2:45 PM, gromacs query wrote:
>>
>> Aha! thanks Erik (and Justin),
>>>
>>> I really feel sorry 35 and 135 will be removed by sed. I must have given a
>>> thought about that. So this was reason sed was over doing the things. Also
>>> as you asked: They are random residue number water molecules so
>>> not continuous and they were selected on the criteria based on X Y Z
>>> coordinates (some space fixed and outlier waters are to be removed)
>>>
>>> regards,
>>>
>>>
>>> On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund <erikm at xray.bmc.uu.se>
>>> wrote:
>>>
>>>
>>>> On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:
>>>>
>>>>
>>>> On Mar 1, 2013, at 1:58 PM, gromacs query wrote:
>>>>>
>>>>> Dear Erik,
>>>>>
>>>>>>
>>>>>> so you can filter out the unwanted residues there instead of using an
>>>>>>
>>>>>>>
>>>>>>>> index file.
>>>>>>>
>>>>>>
>>>>>> There are thousands of water to be removed so simple commands like sed
>>>>>> exhausts when I run it in loops. e.g. Just to say :
>>>>>>
>>>>>> sed -e '/35SOL/d' -e '/36SOL/d' -e '/38SOL/d' -e '/39SOL/d' -e
>>>>>> '/40SOL/d'
>>>>>> -e '/41SOL/d' -e '/42SOL/d' -e '/43SOL/d' -e '/44SOL/d' -e '/45SOL/d'
>>>>>> old.gro > new2.gro
>>>>>>
>>>>>> this will remove such 10 residues but if you run this again and again
>>>>>> (in
>>>>>> text exe format) say 1000 times it exhausts some how and remove waters
>>>>>> which are not even mentioned in sed command! I have checked it many
>>>>>> times.
>>>>>> So I thought if index file could help me. But please reply for point 3:
>>>>>>
>>>>>>
>>>>> First of all, that's not a safe way of removing waters. Note that both
>>>>> SOL 35, SOL 135, ... will be removed by that command. Secondly, I'm sure
>>>>> you can think of a better way of scripting it, using e.g. sed or awk. By
>>>>> which criteria do you select the waters to be removed?
>>>>>
>>>>>
>>>> If its a contiguous chunk then it's dead simple.
>>>>
>>>>
>>>>
>>>>
>>>>> 3) Also once I get index file can editconf help to write a new gro
>>>>>>
>>>>>>>
>>>>>>>>> without the residues mentioned in index file?. I used this
>>>>>>>> editconf -f
>>>>>>>>
>>>>>>> my.gro -n index.ndx -o del.gro .
>>>>>>
>>>>>>
>>>>>> thanks,
>>>>>>
>>>>>> This gave me del.gro having residues mentioned in index file. But I
>>>>>> want
>>>>>> del.gro file without the residues mentioned in index file.
>>>>>>
>>>>>> On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund <erikm at xray.bmc.uu.se>
>>>>>> wrote:
>>>>>>
>>>>>> The ndx format is really simple. You can easily script your way to a
>>>>>> new
>>>>>>
>>>>>>> index group as long as the selection of atoms can be automated.
>>>>>>> Furthermore, the gro format is also simple, so you can filter out the
>>>>>>> unwanted residues there instead of using an index file.
>>>>>>>
>>>>>>> Erik
>>>>>>>
>>>>>>>
>>>>>>> On Mar 1, 2013, at 1:42 PM, gromacs query wrote:
>>>>>>>
>>>>>>> Dear All,
>>>>>>>
>>>>>>>
>>>>>>>> I know the residue numbers of SOL molecules (which are more than
>>>>>>>> thousands)
>>>>>>>> which I want to remove them from a gro file. I searched that make_ndx
>>>>>>>> can
>>>>>>>> be used make a index file to define residues. But It is a prompt
>>>>>>>> based
>>>>>>>> tool
>>>>>>>> and its difficult to type manually thousands of residue numbers.
>>>>>>>>
>>>>>>>> 1) Is there some way to feed the residue numbers to make_ndx? Or I
>>>>>>>> need to
>>>>>>>> make index file format my self by some scritpting Or is there is
>>>>>>>> rather
>>>>>>>> easier way of doing in gromacs.
>>>>>>>>
>>>>>>>> 2) Also is there any direct command which helps to remove a residue
>>>>>>>> number
>>>>>>>> directly from a gro file without using index file input; means
>>>>>>>> residue
>>>>>>>> defined in command itself?
>>>>>>>>
>>>>>>>> 3) Also once I get index file can editconf help to write a new gro
>>>>>>>> without
>>>>>>>> the residues mentioned in index file?. I used this editconf -f my.gro
>>>>>>>> -n
>>>>>>>> index.ndx -o del.gro .
>>>>>>>>
>>>>>>>> This gave me del.gro having residues mentioned in index file. But I
>>>>>>>> want
>>>>>>>> del.gro file without the residues mentioned in index file.
>>>>>>>>
>>>>>>>>
>>>>>>>> regards,
>>>>>>>> --
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>
>------------------------------
>
>Message: 3
>Date: Sat, 2 Mar 2013 21:21:04 +0800 (CST)
>From: "congchen" <congchen at dlut.edu.cn>
>Subject: [gmx-users] Semiisotropic pressure coupling problem
>To: "gmx-users" <gmx-users at gromacs.org>
>Message-ID:
> <10875819.1362230464271.STDYmailserver.webmail126 at mail1.dlut.edu.cn>
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