> 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. 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 > (nik...@tezu.ernet.in) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 27 May 2018 23:00:26 +0330 > From: mostafa paknia <mostafapak...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] topology file > Message-ID: > <CAGEYpLt=sdz8hriyil5cwr45kgc9k9qh0ej4mc90espltnx...@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 <soham9...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] topology file > Message-ID: > <CA+fBeddVdjtivJ1ryR4+QX0+hxTvUOUERPh3ePjbfQaVyfh7=a...@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, <mostafapak...@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! >> >> * 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: 3 > Date: Sun, 27 May 2018 15:51:48 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] topology file > Message-ID: <24fe8b77-6371-8783-cd8c-12bd95f82...@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 > > jalem...@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.di...@nitk.edu.in> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Regarding calculation of SDF > Message-ID: > <CAD6GXy2QsD4szQE87C=L3XMkGEXv=nu3xg+6p2dhjwgu69d...@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. > [image: Mailtrack] > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> > Sender > notified by > Mailtrack > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality5&> > 05/28/18, > 7:47:09 AM > > > ------------------------------ > > Message: 5 > Date: Mon, 28 May 2018 09:24:45 +0530 > From: nik...@tezu.ernet.in > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue > 89 > Message-ID: > <22c52cb804465d3579f68612b19570f3.squir...@webmail.tezu.ernet.in> > Content-Type: text/plain; charset="utf-8" > >> Message: 1 >> Date: Thu, 24 May 2018 17:31:00 +0530 >> From: nik...@tezu.ernet.in >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: [gmx-users] AMP_simulation >> Message-ID: >> <6be73c5ff3ffc470d178638a18b6e33f.squir...@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 <soham9...@gmail.com> >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] AMP_simulation >> Message-ID: >> <ca+fbedf9keoopu-wlqhvegao0denbo+hcb9d4jz6-6thqey...@mail.gmail.com> >> Content-Type: text/plain; charset="UTF-8" >> >> Try with 1ps time step >> >> On Thu, 24 May 2018, 6:33 pm , <nik...@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 <drrahulsur...@gmail.com> >> To: gmx-us...@gromacs.org >> Cc: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: Re: [gmx-users] AMP_simulation >> Message-ID: >> <caatfitsdz0tdtohfcarsvyfmktcgg3tueq07+jtm7vkuwvy...@mail.gmail.com> >> Content-Type: text/plain; charset="UTF-8" >> >> Hi >> >> On Thu, May 24, 2018 at 5:31 PM, <nik...@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 <drrahulsur...@gmail.com> >> To: gmx-us...@gromacs.org >> Cc: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: Re: [gmx-users] AMP_simulation >> Message-ID: >> <caatfitsdz0tdtohfcarsvyfmktcgg3tueq07+jtm7vkuwvy...@mail.gmail.com> >> Content-Type: text/plain; charset="UTF-8" >> >> Hi >> >> On Thu, May 24, 2018 at 5:31 PM, <nik...@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 > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and > destroy it from your system. Though considerable effort has been made to > deliver error free e-mail messages but it can not be guaranteed to be > secure or error-free as information could be intercepted, corrupted, lost, > destroyed, delayed, or may contain viruses. The recipient must verify the > integrity of this e-mail message. > > ------------------------------ > > -- > 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 169, Issue 96 > ****************************************************** > * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- 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.