[gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue 96

Mon May 28 10:03:00 CEST 2018

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> Today's Topics:
>
>    1. topology file (mostafa paknia)
>    2. Re: topology file (Soham Sarkar)
>    3. Re: topology file (Justin Lemkul)
>    4. Regarding calculation of SDF (Dilip.H.N)
>    5. Re: gromacs.org_gmx-users Digest, Vol 169, Issue 89
>       (niki24 at tezu.ernet.in)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 27 May 2018 23:00:26 +0330
> From: mostafa paknia <mostafapaknia at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] topology file
> Message-ID:
> 	<CAGEYpLt=SdZ8hRiYiL5cwR45KGc9K9qH0eJ4Mc90esPLTnxm7g at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> hi
> i need to build just one topology file for two items
> one drug and one carbon nanotube (as drug carrier)
> how can i do that?
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 28 May 2018 01:13:53 +0530
> From: Soham Sarkar <soham9038 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] topology file
> Message-ID:
> 	<CA+fBeddVdjtivJ1ryR4+QX0+hxTvUOUERPh3ePjbfQaVyfh7=A at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Concatenate the drug and the CNT into a songle file by using cat ( see
> multiple protein in a box) renumber the combined gro... then take pdb from
> the gro file and use it as the initial structure.. put in any topology
> building server
>
> On Mon, 28 May 2018, 1:00 am mostafa paknia, <mostafapaknia at gmail.com>
> wrote:
>
>> hi
>> i need to build just one topology file for two items
>> one drug and one carbon nanotube (as drug carrier)
>> how can i do that?
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 27 May 2018 15:51:48 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] topology file
> Message-ID: <24fe8b77-6371-8783-cd8c-12bd95f82196 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 5/27/18 3:30 PM, mostafa paknia wrote:
>> hi
>> i need to build just one topology file for two items
>> one drug and one carbon nanotube (as drug carrier)
>> how can i do that?
>
> The CNT topology can be built with x2top. Anything else has to be
> parametrized with online servers or with whatever protocol the parent
> force field prescribes. The drug topology (.itp) can then be #included
> within the .top file generated for the CNT.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 28 May 2018 07:47:36 +0530
> From: "Dilip.H.N" <cy16f01.dilip at nitk.edu.in>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Regarding calculation of SDF
> Message-ID:
> 	<CAD6GXy2QsD4szQE87C=L3XMkGEXv=nu3xg+6P2dHJwGU69D1jA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
> I want to calculate the Spatial Distribution Function of say N-terminal
> nitrogen atom and all the oxygen atoms of the water molecules.
> So, i have created the index file in which i have the nitrogen atom and
> all
> the oxygen atoms of water molecules. And here are my commands that i gave
> inorder to calculate SDF:
> gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur
> compact
> -pbc whole
> gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit
> rot+trans
> gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10
>
> I get the following:
> Reading file nptmd.tpr, VERSION 2016.2 (single precision)
> Select group to generate SDF:
> Group     0 (             N) has     1 elements
> Group     1 (             OW) has   511 elements
> Select a group: 0
> Selected 0: 'N'
> Select group to output coords (e.g. solute):
> Group     0 (             N) has     1 elements
> Group     1 (             OW) has   511 elements
> Select a group: 1
> Selected 1: 'OW'
> TNG library: Cannot uncompress data block.
> /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
> 5298
> TNG library: Cannot uncompress data block.
> /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
> 5298
> Last frame      60000 time 30000.000
> Back Off! I just backed up grid.cube to ./#grid.cube.1#
> Counts per frame in all 27 cubes divided by 3.703704e-02
> Normalized data: average 1.000000e+00, min 0.000000e+00, max 2.700000e+01
>
>
> and if i view the grid.cube file in vmd, i am unable to get a proper
> SDF/it
> is wired when i give an isovalues and change its values...
>
> How can i solve this..??
> Any suggestions are highly appreciated.
>
> Thank you.
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
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> 05/28/18,
> 7:47:09 AM
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>
> ------------------------------
>
> Message: 5
> Date: Mon, 28 May 2018 09:24:45 +0530
> From: niki24 at tezu.ernet.in
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue
> 	89
> Message-ID:
> 	<22c52cb804465d3579f68612b19570f3.squirrel at webmail.tezu.ernet.in>
> Content-Type: text/plain; charset="utf-8"
>
>> Message: 1
>> Date: Thu, 24 May 2018 17:31:00 +0530
>> From: niki24 at tezu.ernet.in
>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: [gmx-users] AMP_simulation
>> Message-ID:
>> 	<6be73c5ff3ffc470d178638a18b6e33f.squirrel at webmail.tezu.ernet.in>
>> Content-Type: text/plain;charset=utf-8
>>
>> Hello,
>>
>> I have tried doing the Molecular dynamics simulation of AMP using the
>> Gromos54a7 forcefield.
>>
>> ITP parameters for the AMP molecule has been generated using the ATB
>> builder. Minimization of the molecule goes on well however while
>> carrying
>> out the Nvt theres a segmantation fault resulting in step files.
>>
>> Moreover LINCS warning are shown with bonds that rotated more than 30
>> degrees. ihave tried changing lincs parameter and also increasing the
>> step
>> size, but still simulation crashes.
>>
>> Is it suggestible to generate topology for the AMP molecule from the
>> available topological parameters of ATP in GROMACS. Or are their any
>> source of getting the correct itp paremeters for "AMP".
>>
>> Thanks
>> Nikita Bora
>>
>>
>
>>
>> Message: 2
>> Date: Thu, 24 May 2018 18:38:53 +0530
>> From: Soham Sarkar <soham9038 at gmail.com>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] AMP_simulation
>> Message-ID:
>> 	<CA+fBedf9KeoopU-wLqhVEGaO0DeNbo+HCb9d4Jz6-6tHQEY9yw at mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Try with 1ps time step
>>
>> On Thu, 24 May 2018, 6:33 pm , <niki24 at tezu.ernet.in> wrote:
>>
>>> Hello,
>>>
>>> I have tried doing the Molecular dynamics simulation of AMP using the
>>> Gromos54a7 forcefield.
>>>
>>> ITP parameters for the AMP molecule has been generated using the ATB
>>> builder. Minimization of the molecule goes on well however while
>>> carrying
>>> out the Nvt theres a segmantation fault resulting in step files.
>>>
>>> Moreover LINCS warning are shown with bonds that rotated more than 30
>>> degrees. ihave tried changing lincs parameter and also increasing the
>>> step
>>> size, but still simulation crashes.
>>>
>>> Is it suggestible to generate topology for the AMP molecule from the
>>> available topological parameters of ATP in GROMACS. Or are their any
>>> source of getting the correct itp paremeters for "AMP".
>>>
>>> Thanks
>>> Nikita Bora
>>>
>>>
>>>
>>
>> Message: 3
>> Date: Thu, 24 May 2018 18:43:01 +0530
>> From: RAHUL SURESH <drrahulsuresh at gmail.com>
>> To: gmx-users at gromacs.org
>> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: Re: [gmx-users] AMP_simulation
>> Message-ID:
>> 	<CAAtfiTsdz0TDtoHfCArSVyFmKTcGG3tUeQ07+jtm7vKuwvYomQ at mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Hi
>>
>> On Thu, May 24, 2018 at 5:31 PM, <niki24 at tezu.ernet.in> wrote:
>>
>>> Hello,
>>>
>>> I have tried doing the Molecular dynamics simulation of AMP using the
>>> Gromos54a7 forcefield.
>>>
>>> ITP parameters for the AMP molecule has been generated using the ATB
>>> builder. Minimization of the molecule goes on well however while
>>> carrying
>>> out the Nvt theres a segmantation fault resulting in step files.
>>>
>>
>> Segmentation fault normally occurs for large system with small memory.
>> You
>> can write xtc which is a compresssed trajectory file.
>> Adding time steps to write the file.
>>
>>>
>>> Moreover LINCS warning are shown with bonds that rotated more than 30
>>> degrees. ihave tried changing lincs parameter and also increasing the
>>> step
>>> size, but still simulation crashes.
>>>
>>
>> Lincs warning, as for here without knowing exactly about the system, i
>> think the error is due to improper minimization.
>> Minimize properly ir go for double precision method.
>>
>>>
>>> Is it suggestible to generate topology for the AMP molecule from the
>>> available topological parameters of ATP in GROMACS. Or are their any
>>> source of getting the correct itp paremeters for "AMP".
>>>
>>
>> Yeah, not an issue I guess.
>>
>>>
>>> Thanks
>>> Nikita Bora
>>>
>>
>> Thanks back
>>
> -
>> *Regards,*
>> *Rahul *
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Thu, 24 May 2018 18:43:01 +0530
>> From: RAHUL SURESH <drrahulsuresh at gmail.com>
>> To: gmx-users at gromacs.org
>> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: Re: [gmx-users] AMP_simulation
>> Message-ID:
>> 	<CAAtfiTsdz0TDtoHfCArSVyFmKTcGG3tUeQ07+jtm7vKuwvYomQ at mail.gmail.com>
>> Content-Type: text/plain; charset="UTF-8"
>>
>> Hi
>>
>> On Thu, May 24, 2018 at 5:31 PM, <niki24 at tezu.ernet.in> wrote:
>>
>>> Hello,
>>>
>>> I have tried doing the Molecular dynamics simulation of AMP using the
>>> Gromos54a7 forcefield.
>>>
>>> ITP parameters for the AMP molecule has been generated using the ATB
>>> builder. Minimization of the molecule goes on well however while
>>> carrying
>>> out the Nvt theres a segmantation fault resulting in step files.
>>>
>>
>> Segmentation fault normally occurs for large system with small memory.
>> You
>> can write xtc which is a compresssed trajectory file.
>> Adding time steps to write the file.
>>
>>>
>>> Moreover LINCS warning are shown with bonds that rotated more than 30
>>> degrees. ihave tried changing lincs parameter and also increasing the
>>> step
>>> size, but still simulation crashes.
>>>
>>
>> Lincs warning, as for here without knowing exactly about the system, i
>> think the error is due to improper minimization.
>> Minimize properly ir go for double precision method.
>>
>>>
>>> Is it suggestible to generate topology for the AMP molecule from the
>>> available topological parameters of ATP in GROMACS. Or are their any
>>> source of getting the correct itp paremeters for "AMP".
>>>
>>
>> Yeah, not an issue I guess.
>>
>>>
>>> Thanks
>>> Nikita Bora
>>>
>>
>> Thanks back
>> --
>> *Regards,*
>> *Rahul *
>>
>>
>>
> Hello,
> Thanks for your suggestions, i have attached herewith the coordinate file
> of amp and also the itp file.
>
> If i could get any suggestion whether the itp file generated is correct
> for my molecule.
>
The mentioned files has been attached in this droplink

https://www.dropbox.com/sh/2ql8wvle0grkr8t/AABjeFRMPg7_w5HK1gLdu2jja?dl=0

> Thanks
> Nikita Bora
>
>
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