> 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: 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" <jalem...@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@gromacs.org> > Message-ID: <4fafeb85.20...@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" <jalem...@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@gromacs.org> > Message-ID: <4fafebf6.8040...@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 <jalem...@vt.edu> >> *To:* Discussion list for GROMACS users <gmx-users@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 <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org >> <mailto:gmx-users@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@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> > <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@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@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@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_arasteh2...@yahoo.com> > Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in > residue pairs > To: "jalem...@vt.edu" <jalem...@vt.edu>, Discussion list for GROMACS > users <gmx-users@gromacs.org> > Message-ID: > <1336929612.41916.yahoomail...@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 <jalem...@vt.edu> > To: Discussion list for GROMACS users <gmx-users@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 <jalem...@vt.edu> >> *To:* Discussion list for GROMACS users <gmx-users@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 <jalem...@vt.edu <mailto:jalem...@vt.edu>> >>? > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org >> <mailto:gmx-users@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@gromacs.org >><mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >>? > <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@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@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@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@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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120513/de8323ff/attachment.html > > ------------------------------ > > -- > 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! > > End of gmx-users Digest, Vol 97, Issue 87 > ***************************************** > Sangita Kachhap SRF BIC,IMTECH CHANDIGARH ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- 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
