[gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.
Sangita Kachhap
sangita at imtech.res.in
Mon May 14 05:57:37 CEST 2012
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> Today's Topics:
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> 1. Re: How to get md_0_2. prefix for all output files during
> entexding production run, like got during first run md_0_1.
> (Justin A. Lemkul)
> 2. Re: Fatal error: No atoms found in .rtp file in residue pairs
> (Justin A. Lemkul)
> 3. Re: Fatal error: No atoms found in .rtp file in residue pairs
> (Shima Arasteh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 13 May 2012 13:12:37 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] How to get md_0_2. prefix for all output
> files during entexding production run, like got during first run
> md_0_1.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FAFEB85.20401 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> On 5/13/12 12:52 PM, Sangita Kachhap wrote:
>> Hello all
>>
>> I am running GROMACS Tutorial: KALP15 in POPC
>> I have compeleted production run 1 ns now I want to extend it for next 1 ns.
>> For this I have used commond:
>>
>> tpbconv -s md_0_1.tpr -extend 1000 -o md_0_2.tpr
>> mdrun -s nmd_0_2.tpr -cpi md_0_1.cpt
>>
>> I am getting files are:
>> ener.edr
>> md.log
>> state.cpt
>> state_prev.cpt
>> traj.trr
>> traj.xtc
>> confout.gro
>>
>> During first 1 ns production I have got all files with prefix md_0_1.
>> How I can get it (prefix md_0_2. for all the above files)in next 1 ns
>> production
>> run.
>>
>> Anyone please suggest.
>>
>
> Note the use of -deffnm in the tutorial to set default output names. If you
> want your files to be called "md_0_2.(extension)" then you need to run:
>
> mdrun -deffnm md_0_2 -cpi md_0_1.cpt
Thanks for reply its running fine now.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 13 May 2012 13:14:30 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in
> residue pairs
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FAFEBF6.8040800 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 5/13/12 1:06 PM, Shima Arasteh wrote:
>> Even in gromos87, if I want to make a .rtp file for formyl, I need to put H
>> atom
>> in it? I mean, defining all atoms of a residue is necessary? Aren't the
>> hydrogen
>> atoms set by the gromacs package?
>>
>
> No. The presence of hydrogen atoms is set by the force field, not the software
> that makes use of the force fields. In the Gromos force fields (and I certainly
> hope you're not using Gromos87, as it is ancient and better options are
> available), polar H atoms are explicitly represented. In the case of an
> aldehyde, I would strongly suspect you need an explicit H. I believe there have
> been recent publications regarding extensions of Gromos96 (note, NOT Gromos87)
> that include such organic groups. Using those parameters may speed your
> progress. If my recollection is incorrect and such parameters do not exist, you
> need to derive them yourself.
>
> -Justin
>
>> Cheers,
>> Shima
>>
>> --------------------------------------------------------------------------------
>> *From:* Justin A. Lemkul <jalemkul at vt.edu>
>> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
>> *Sent:* Sunday, May 13, 2012 8:36 PM
>> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
>> pairs
>>
>>
>>
>> On 5/13/12 11:43 AM, Shima Arasteh wrote:
>> > Again thanks for all your replies.
>> > As I got through your advices, I found that the atoms contribute in making
>> bonds
>> > and angles in a residue , or make dihedrals in a residue ( or with atoms in
>> next
>> > ones) plus the charge of a the residue should be defined properly in .rtp
>> files
>> > to define the new residue in aminoacid.rtp file of CHARMM36 force field.
>> > So I arranged this lines to define formyl in .rtp file. And I got the
>> topology.
>> > But there are some questions for me here:
>> >
>> > 1. How can I be sure the formyl which I defined is correct? Is getting the
>> > topology is enough to be sure of the correct output?
>> >
>>
>> It is incorrect. As I said before, a formyl group is an aldehyde and has an H
>> atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group
>> with an incomplete carbon valence.
>>
>> http://en.wikipedia.org/wiki/Aldehyde
>>
>> > The .rtp file for formyl is as below:
>> > [ For ]
>> > [ atoms ]
>> > ; name type charge chargegroup
>> > C CTL1 0.5700 0
>> > O O -0.5700 0
>> > [angles ]
>> > ai aj ak
>> > O C +N
>> > [ bonds ]
>> > C O
>> > C +N
>> >
>> > [ dihedrals ]
>> > O C +N +CA
>> >
>>
>> Aside from the missing atom (and resulting missing bonds, angles, and
>> dihedral),
>> the format of this entry is OK.
>>
>> > 2. There are lots of numbers in .itp file which I got through the
>> swissparam.
>> > But I think the charge of atoms may be useful in this file and also I can
>> just
>> > find the atoms contribute in bonds and angles and.... . Am I right? Or I
>> may get
>> > some other useful information which I can get through the files of
>> swissparam?
>> >
>>
>> If the existing bonded parameters for each interaction type (in ffbonded.itp)
>> are sufficient for defining these interactions, then you can omit the content
>> of
>> the .itp file you've been using in the .rtp entry and rely on the force field
>> to
>> look up those values. There may be some interactions that are not in agreement
>> (or do not exist), in which case you need to either define these parameters in
>> the .rtp entry itself or in ffbonded.itp so that they will be detected by
>> grompp
>> later.
>>
>> -Justin
>>
>> > Thanks in advance, and sorry for disturbing you friends.
>> > Shima
>> >
>> > --------------------------------------------------------------------------------
>> > *From:* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>> > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>>
>> > *Sent:* Saturday, May 12, 2012 10:12 PM
>> > *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
>> residue pairs
>> >
>> >
>> >
>> > On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
>> > >
>> > >
>> > > On 5/12/12 1:32 PM, Shima Arasteh wrote:
>> > >> Dear gmx users,
>> > >>
>> > >> I want to simulate a peptide in water. The peptide has a formyl residue
>> as the
>> > >> N-terminus. I got the parameters of it and then add it to the .rtp file
>> of
>> > >> charmm36.ff as below:
>> > >>
>> > >> [ For ]
>> > >> [ atoms ]
>> > >> ; name type charge chargegroup
>> > >> C C 0.4500 0
>> > >> O O -0.5700 0
>> > >> [ bonds ]
>> > >> ; ai aj fu b0 kb, b0 kb
>> > >> 1 2 1 0.12220 779866.6 0.12220 779866.6
>> > >>
>> > >> [ pairs ]
>> > >> ; ai aj fu
>> > >>
>> > >> [ angles ]
>> > >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
>> > >> 2 1 3 1 123.4390 403.48 123.4390 403.48
>> > >> 2 1 4 1 123.4390 403.48 123.4390 403.48
>> > >>
>> > >> [ dihedrals ]
>> > >> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
>> > >>
>> > >> But when I do what I described, I face this fatal error:
>> > >> Fatal error:
>> > >> No atoms found in .rtp file in residue pairs
>> > >>
>> > >> Would you help me with this problem? Did I add the formyl in a wrong
>> way?
>> > >>
>> > >
>> > > Your [pairs] directive is empty, hence the error. Your [dihedrals]
>> directive
>> > > will also produce the same error. There are no possible pairs in a unit
>> > > containing so few atoms, so you don't even need this. You may need to
>> define
>> > > dihedrals, however, but they also depend upon the next residue.
>> > >
>> > > You also have several other mistakes:
>> > >
>> > > 1. A formyl group has a proton on it; yours has none
>> > > 2. Your net charge on the formyl group is not zero, though this may or
>> may not
>> > > be a consequence of point #1
>> > > 3. There is no connectivity information for linking to the next residue,
>> which
>> > > will mean the formyl group will not be chemically bonded. This also
>> affects
>> your
>> > > dihedrals.
>> > >
>> >
>> > Another that I just caught as I hit send:
>> >
>> > 4. In your [bonds] and [angles] directives, you use atom numbers - they
>> should
>> > be names
>> >
>> > -Justin
>> >
>> > --
>> > ========================================
>> >
>> > Justin A. Lemkul, Ph.D.
>> > Department of Biochemistry
>> > Virginia Tech
>> > Blacksburg, VA
>> > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> > ========================================
>> > --
>> > gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto: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
>> <mailto:gmx-users-request at gromacs.org>
>> > <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>>.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> >
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org <mailto: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
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 13 May 2012 10:20:12 -0700 (PDT)
> From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
> Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in
> residue pairs
> To: "jalemkul at vt.edu" <jalemkul at vt.edu>, Discussion list for GROMACS
> users <gmx-users at gromacs.org>
> Message-ID:
> <1336929612.41916.YahooMailNeo at web36403.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> ?
> Thanks,
> It was just a question and I prefer to use the CHARMM36.
>
>
> ________________________________
> From: Justin A. Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Sunday, May 13, 2012 9:44 PM
> Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
> pairs
>
>
>
> On 5/13/12 1:06 PM, Shima Arasteh wrote:
>> Even in gromos87, if I want to make a .rtp file for formyl, I need to put H
>> atom
>> in it? I mean, defining all atoms of a residue is necessary? Aren't the
>> hydrogen
>> atoms set by the gromacs package?
>>
>
> No.? The presence of hydrogen atoms is set by the force field, not the software
> that makes use of the force fields.? In the Gromos force fields (and I certainly
> hope you're not using Gromos87, as it is ancient and better options are
> available), polar H atoms are explicitly represented.? In the case of an
> aldehyde, I would strongly suspect you need an explicit H.? I believe there have
> been recent publications regarding extensions of Gromos96 (note, NOT Gromos87)
> that include such organic groups.? Using those parameters may speed your
> progress.? If my recollection is incorrect and such parameters do not exist, you
> need to derive them yourself.
>
> -Justin
>
>> Cheers,
>> Shima
>>
>> --------------------------------------------------------------------------------
>> *From:* Justin A. Lemkul <jalemkul at vt.edu>
>> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
>> *Sent:* Sunday, May 13, 2012 8:36 PM
>> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
>> pairs
>>
>>
>>
>> On 5/13/12 11:43 AM, Shima Arasteh wrote:
>>? > Again thanks for all your replies.
>>? > As I got through your advices, I found that the atoms contribute in making
>> bonds
>>? > and angles in a residue , or make dihedrals in a residue ( or with atoms in
>> next
>>? > ones) plus the charge of a the residue should be defined properly in .rtp
>> files
>>? > to define the new residue in aminoacid.rtp file of CHARMM36 force field.
>>? > So I arranged this lines to define formyl in .rtp file. And I got the
>> topology.
>>? > But there are some questions for me here:
>>? >
>>? > 1. How can I be sure the formyl which I defined is correct? Is getting the
>>? > topology is enough to be sure of the correct output?
>>? >
>>
>> It is incorrect. As I said before, a formyl group is an aldehyde and has an H
>> atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group
>> with an incomplete carbon valence.
>>
>> http://en.wikipedia.org/wiki/Aldehyde
>>
>>? > The .rtp file for formyl is as below:
>>? > [ For ]
>>? > [ atoms ]
>>? > ; name type charge chargegroup
>>? > C CTL1 0.5700 0
>>? > O O -0.5700 0
>>? > [angles ]
>>? > ai aj ak
>>? > O C +N
>>? > [ bonds ]
>>? > C O
>>? > C +N
>>? >
>>? > [ dihedrals ]
>>? > O C +N +CA
>>? >
>>
>> Aside from the missing atom (and resulting missing bonds, angles, and
>> dihedral),
>> the format of this entry is OK.
>>
>>? > 2. There are lots of numbers in .itp file which I got through the
>> swissparam.
>>? > But I think the charge of atoms may be useful in this file and also I can
>> just
>>? > find the atoms contribute in bonds and angles and.... . Am I right? Or I
>> may get
>>? > some other useful information which I can get through the files of
>> swissparam?
>>? >
>>
>> If the existing bonded parameters for each interaction type (in ffbonded.itp)
>> are sufficient for defining these interactions, then you can omit the content
>> of
>> the .itp file you've been using in the .rtp entry and rely on the force field
>> to
>> look up those values. There may be some interactions that are not in agreement
>> (or do not exist), in which case you need to either define these parameters in
>> the .rtp entry itself or in ffbonded.itp so that they will be detected by
>> grompp
>> later.
>>
>> -Justin
>>
>>? > Thanks in advance, and sorry for disturbing you friends.
>>? > Shima
>>? >
>>? >
>> --------------------------------------------------------------------------------
>>? > *From:* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>? > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>>
>>? > *Sent:* Saturday, May 12, 2012 10:12 PM
>>? > *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in
>> residue pairs
>>? >
>>? >
>>? >
>>? > On 5/12/12 1:37 PM, Justin A. Lemkul wrote:
>>? > >
>>? > >
>>? > > On 5/12/12 1:32 PM, Shima Arasteh wrote:
>>? > >> Dear gmx users,
>>? > >>
>>? > >> I want to simulate a peptide in water. The peptide has a formyl residue
>> as the
>>? > >> N-terminus. I got the parameters of it and then add it to the .rtp file
>> of
>>? > >> charmm36.ff as below:
>>? > >>
>>? > >> [ For ]
>>? > >> [ atoms ]
>>? > >> ; name type charge chargegroup
>>? > >> C C 0.4500 0
>>? > >> O O -0.5700 0
>>? > >> [ bonds ]
>>? > >> ; ai aj fu b0 kb, b0 kb
>>? > >> 1 2 1 0.12220 779866.6 0.12220 779866.6
>>? > >>
>>? > >> [ pairs ]
>>? > >> ; ai aj fu
>>? > >>
>>? > >> [ angles ]
>>? > >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
>>? > >> 2 1 3 1 123.4390 403.48 123.4390 403.48
>>? > >> 2 1 4 1 123.4390 403.48 123.4390 403.48
>>? > >>
>>? > >> [ dihedrals ]
>>? > >> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult
>>? > >>
>>? > >> But when I do what I described, I face this fatal error:
>>? > >> Fatal error:
>>? > >> No atoms found in .rtp file in residue pairs
>>? > >>
>>? > >> Would you help me with this problem? Did I add the formyl in a wrong
>> way?
>>? > >>
>>? > >
>>? > > Your [pairs] directive is empty, hence the error. Your [dihedrals]
>> directive
>>? > > will also produce the same error. There are no possible pairs in a unit
>>? > > containing so few atoms, so you don't even need this. You may need to
>> define
>>? > > dihedrals, however, but they also depend upon the next residue.
>>? > >
>>? > > You also have several other mistakes:
>>? > >
>>? > > 1. A formyl group has a proton on it; yours has none
>>? > > 2. Your net charge on the formyl group is not zero, though this may or
>> may not
>>? > > be a consequence of point #1
>>? > > 3. There is no connectivity information for linking to the next residue,
>> which
>>? > > will mean the formyl group will not be chemically bonded. This also
>> affects
>> your
>>? > > dihedrals.
>>? > >
>>? >
>>? > Another that I just caught as I hit send:
>>? >
>>? > 4. In your [bonds] and [angles] directives, you use atom numbers - they
>> should
>>? > be names
>>? >
>>? > -Justin
>>? >
>>? > --
>>? > ========================================
>>? >
>>? > Justin A. Lemkul, Ph.D.
>>? > Department of Biochemistry
>>? > Virginia Tech
>>? > Blacksburg, VA
>>? > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>? > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>? >
>>? > ========================================
>>? > --
>>? > gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto: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
>> <mailto:gmx-users-request at gromacs.org>
>>? > <mailto:gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>>.
>>? > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>? >
>>? >
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org <mailto: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
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> 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
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> End of gmx-users Digest, Vol 97, Issue 87
> *****************************************
>
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
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