[gmx-users] No such moleculetype NA+
YUVRAJ UBOVEJA
yuvrajthedon at gmail.com
Sun Dec 26 10:33:55 CET 2010
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-request at gromacs.org> wrote:
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> Today's Topics:
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> 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 <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at 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-bounces at 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
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>>> Please do not use, copy or disclose the information contained in this
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>>> 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
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>>> computer system: you are advised to perform your own checks. Email
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>>>
>>> >>
>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell& Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se<
>> http://folding.bmc.uu.se/>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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>>
>> << 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
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> ---------- Forwarded message ----------
> From: "NG HUI WEN" <HuiWen.Ng at nottingham.edu.my>
> To: "Discussion list for GROMACS users" <gmx-users at 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-bounces at 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-bounces at 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.
> > spoel at xray.bmc.uu.se http://folding.bmc.uu.se<
> http://folding.bmc.uu.se/>
> > --
> > gmx-users mailing list gmx-users at 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-request at 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
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> --
> gmx-users mailing list gmx-users at 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-request at 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.lakshmi at research.iiit.ac.in>
> To: Discussion list for GROMACS users <gmx-users at 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 <shikhaiiitabi at gmail.com>
> To: gmx-users at 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 at 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
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