Hello Shikha Replace NA+ with NA in your topol.top file. It will solve the problem as it recognise NA for NA+.
Thanks Yuvraj IIIT Hyderabad On Sun, Dec 26, 2010 at 12:26 PM, <gmx-users-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > Today's Topics: > > 1. Re: Replicating an experiment (David van der Spoel) > 2. RE: Replicating an experiment (NG HUI WEN) > 3. average pressure too high (sreelakshmi ramesh) > 4. No such moleculetype NA+ (shikha agarwal) > > > ---------- Forwarded message ---------- > From: David van der Spoel <sp...@xray.bmc.uu.se> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Date: Sat, 25 Dec 2010 22:55:34 +0100 > Subject: Re: [gmx-users] Replicating an experiment > On 12/25/10 6:37 PM, NG HUI WEN wrote: > >> Thank you David for your prompt and useful reply :) I am in fact >> simulating a membrane protein. >> >> It's good to know I can use the "generate-new-starting-velocity" method. >> But, do you mind to elaborate a bit more what you mean by "if you simulate >> long enough"? >> >> I would like to try your suggestion of picking a random structure from an >> elevated temperature simulation. Can I achieve that by taking my existing >> membrane protein system, >> 1) pass it through grompp with a new mdp (with higher temperature) to >> produce a new .tpr file >> 2) simulate the system for a period (perhaps 1 ns) >> 3) take any frame / final structure >> 4) pass it through grompp again (with original mdp with temperature 300K, >> gen_seed = -1) to produce the .tpr file for my replicate? >> >> Yes that is what I meant. Of course you should check that your protein is > not unfolding, or you membrane going into the wrong phase. > > Thanks very much indeed!! >> >> ________________________________ >> >> From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel >> Sent: Sat 12/25/2010 10:28 PM >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] Replicating an experiment >> >> >> >> On 2010-12-25 15.05, NG HUI WEN wrote: >> >>> Dear all, >>> Merry Xmas! I have a very quick question here which i'd like to pick >>> your brain on, would really appreciate a reply. >>> I am planning to replicate an experiment that I have carried out. Just >>> wondering what is the best way to do it? I am thinking of changing the >>> starting velocity of my system by setting a random number e.g 23412445 >>> etc in the gen_seed section as below, not sure if it is meaningful to do >>> so? >>> gen_vel = yes >>> gen_temp = 300.0 >>> gen_seed = random number >>> Thank you for your input! >>> >> That will work fine, if you simulate long enough. Consider that the >> starting structure may also influence how different your results will >> be, e.g. for a protein in water. For liquids there is no such problem. >> You can do a simulation and slightly elevated temperature and pick >> structures from that with a different random seed, in order to randomize >> your simulations even more. >> >>> HW >>> << >>> >>> This message and any attachment are intended solely for the addressee >>> and may contain confidential information. If you have received this >>> message in error, please send it back to me, and immediately delete it. >>> Please do not use, copy or disclose the information contained in this >>> message or in any attachment. Any views or opinions expressed by the >>> author of this email do not necessarily reflect the views of the >>> University of Nottingham. >>> >>> This message has been checked for viruses but the contents of an >>> attachment may still contain software viruses which could damage your >>> computer system: you are advised to perform your own checks. Email >>> communications with the University of Nottingham may be monitored as >>> permitted by UK& Malaysia legislation. >>> >>> >> >>> >>> >> >> -- >> David van der Spoel, Ph.D., Professor of Biology >> Dept. of Cell& Molec. Biol., Uppsala University. >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >> sp...@xray.bmc.uu.se http://folding.bmc.uu.se< >> http://folding.bmc.uu.se/> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> >> >> << This message and any attachment are intended solely for the addressee >> and may contain confidential information. If you have received this message >> in error, please send it back to me, and immediately delete it. Please do >> not use, copy or disclose the information contained in this message or in >> any attachment. Any views or opinions expressed by the author of this email >> do not necessarily reflect the views of the University of Nottingham. >> >> This message has been checked for viruses but the contents of an >> attachment may still contain software viruses which could damage your >> computer system: you are advised to perform your own checks. Email >> communications with the University of Nottingham may be monitored as >> permitted by UK& Malaysia legislation.>> >> >> > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > > ---------- Forwarded message ---------- > From: "NG HUI WEN" <huiwen...@nottingham.edu.my> > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Sun, 26 Dec 2010 09:46:05 +0800 > Subject: RE: [gmx-users] Replicating an experiment > > Got it, thanks very much David! > > :) > > -----Original Message----- > From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel > Sent: Sun 12/26/2010 5:55 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Replicating an experiment > > On 12/25/10 6:37 PM, NG HUI WEN wrote: > > Thank you David for your prompt and useful reply :) I am in fact > simulating a membrane protein. > > > > It's good to know I can use the "generate-new-starting-velocity" method. > But, do you mind to elaborate a bit more what you mean by "if you simulate > long enough"? > > > > I would like to try your suggestion of picking a random structure from an > elevated temperature simulation. Can I achieve that by taking my existing > membrane protein system, > > 1) pass it through grompp with a new mdp (with higher temperature) to > produce a new .tpr file > > 2) simulate the system for a period (perhaps 1 ns) > > 3) take any frame / final structure > > 4) pass it through grompp again (with original mdp with temperature 300K, > gen_seed = -1) to produce the .tpr file for my replicate? > > > Yes that is what I meant. Of course you should check that your protein > is not unfolding, or you membrane going into the wrong phase. > > > Thanks very much indeed!! > > > > ________________________________ > > > > From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel > > Sent: Sat 12/25/2010 10:28 PM > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Replicating an experiment > > > > > > > > On 2010-12-25 15.05, NG HUI WEN wrote: > >> Dear all, > >> Merry Xmas! I have a very quick question here which i'd like to pick > >> your brain on, would really appreciate a reply. > >> I am planning to replicate an experiment that I have carried out. Just > >> wondering what is the best way to do it? I am thinking of changing the > >> starting velocity of my system by setting a random number e.g 23412445 > >> etc in the gen_seed section as below, not sure if it is meaningful to do > so? > >> gen_vel = yes > >> gen_temp = 300.0 > >> gen_seed = random number > >> Thank you for your input! > > That will work fine, if you simulate long enough. Consider that the > > starting structure may also influence how different your results will > > be, e.g. for a protein in water. For liquids there is no such problem. > > You can do a simulation and slightly elevated temperature and pick > > structures from that with a different random seed, in order to randomize > > your simulations even more. > >> HW > >> << > >> > >> This message and any attachment are intended solely for the addressee > >> and may contain confidential information. If you have received this > >> message in error, please send it back to me, and immediately delete it. > >> Please do not use, copy or disclose the information contained in this > >> message or in any attachment. Any views or opinions expressed by the > >> author of this email do not necessarily reflect the views of the > >> University of Nottingham. > >> > >> This message has been checked for viruses but the contents of an > >> attachment may still contain software viruses which could damage your > >> computer system: you are advised to perform your own checks. Email > >> communications with the University of Nottingham may be monitored as > >> permitted by UK& Malaysia legislation. > >> > >> >> > >> > > > > > > -- > > David van der Spoel, Ph.D., Professor of Biology > > Dept. of Cell& Molec. Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > > sp...@xray.bmc.uu.se http://folding.bmc.uu.se< > http://folding.bmc.uu.se/> > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > > > > << This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this message > in error, please send it back to me, and immediately delete it. Please do > not use, copy or disclose the information contained in this message or in > any attachment. Any views or opinions expressed by the author of this email > do not necessarily reflect the views of the University of Nottingham. > > > > This message has been checked for viruses but the contents of an > attachment may still contain software viruses which could damage your > computer system: you are advised to perform your own checks. Email > communications with the University of Nottingham may be monitored as > permitted by UK& Malaysia legislation.>> > > > > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > << This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this message > in error, please send it back to me, and immediately delete it. Please do > not use, copy or disclose the information contained in this message or in > any attachment. Any views or opinions expressed by the author of this email > do not necessarily reflect the views of the University of Nottingham. > > This message has been checked for viruses but the contents of an attachment > may still contain software viruses which could damage your computer system: > you are advised to perform your own checks. Email communications with the > University of Nottingham may be monitored as permitted by UK & Malaysia > legislation. >> > > > ---------- Forwarded message ---------- > From: sreelakshmi ramesh <sree.laks...@research.iiit.ac.in> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Date: Sun, 26 Dec 2010 10:58:12 +0530 > Subject: [gmx-users] average pressure too high > Dear users, > I did nvt equil and after that npt equilbriation and i am > using parinello rahman as the barostat but the prob is even after 200 ps of > equil the avg pressure is 1.5 bar .can anybody hepl me out with the > issue.Any suggestions please. > > sree. > > > ---------- Forwarded message ---------- > From: shikha agarwal <shikhaiiit...@gmail.com> > To: gmx-users@gromacs.org > Date: Sun, 26 Dec 2010 12:26:16 +0530 > Subject: [gmx-users] No such moleculetype NA+ > hello , > > this is my ions.itp file for gromos53a6 forcefield > > [ moleculetype ] > ; molname nrexcl > CU1 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 CU1+ 1 CU1 CU 1 1 63.54600 > > [ moleculetype ] > ; molname nrexcl > CU 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 CU2+ 1 CU CU 1 2 63.54600 > > [ moleculetype ] > ; molname nrexcl > ZN 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 ZN2+ 1 ZN ZN 1 2 65.37000 > this is my ions.itp > > [ moleculetype ] > ; molname nrexcl > MG 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 MG2+ 1 MG MG 1 2 24.30500 > > [ moleculetype ] > ; molname nrexcl > CA 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 CA2+ 1 CA CA 1 2 40.08000 > > [ moleculetype ] > ; molname nrexcl > NA 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 NA+ 1 NA NA 1 1 22.9898 > > [ moleculetype ] > ; molname nrexcl > CL 1 > > [ atoms ] > ; id at type res nr residu name at name cg nr charge > mass > 1 CL- 1 CL CL 1 -1 35.45300 > > > > > for adding ions I used this command ... > > genion -s ions.tpr -o system_solv_ions.gro -p grompp.top -pname NA+ -np 11 > -nname CL- > > now when I m doing EM then getting this error > > grompp -f minim.mdp -c system_solv_ions.gro -p grompp.top -o em.tpr > > Fatal error: > No such moleculetype NA+ > > > help me ! > > regards: > shikha > > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > -- Yuvraj Uboveja M.Tech. Bioinformatics IIIT Hyderabad
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists