Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond
On the same topic, Espinoza et al. also developed a good estimator for HB energy. See E. Espinosa, E. Molins, C. Lecomte, Chem. Phys. Lett., 285 (1998), p. 170. 31 maj 2012 kl. 16.51 skrev ABEL Stephane 175950: Hi, Here, my 2 cents worth. You can also estimate (roughly !!) the HB energy between two groups (say NH---CO) by using the Kabsch and Sander function described in Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577−2637). Quoting: E = qlq2(1/r(0N) + l/r(CH) - l/r(OH) - l/r(CN))*f with q1 = 0.42e and q 2 = 0.20e, e being the unit electron charge and r(AB) the interatomic distance from A to B. In chemical units, r is in angstroms, the dimensional factor f = 332, and E is in kcal/mol. A good H bond has about -3 kcal/mol binding energy. We choose a generous cutoff to allow for bifurcated H bonds and errors in coordinates and assign an H bond between C=O of residue i and N-H of residue j if E is less than the cutoff, i.e., “Hbond(ij)=: [E -0.5kcal/mole].” To obtain HB energy value E, you need only the distance between the donnor and acceptor groups. HTH Stephane -- Message: 2 Date: Thu, 31 May 2012 15:00:05 +0200 From: lloyd riggs lloyd.ri...@gmx.ch Subject: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 20120531130005.302...@gmx.net Content-Type: text/plain; charset=utf-8 Dear All, I have no clue what specifically you are trying, but I feal bad for all the physicist and quantum chemist whom have provided the software and continued to develop it. Scanning in my free time, it seems a large amount of confusion on what people are trying to do stems from differences in what is taught textbook wise for things. For instance a hydrogen bond to a physicist is an integration over space in 3 dimensions including time and probabilities of occupied spaces (atom position variabilities reflected even more in proteins, ie the necessity of multiple MD runs with different starting conformations), Vs. an organic chemist whom has cut offs, ie angles between two points and set distances between two atoms which generally reflect the means of calculated chemical energies within a range (say 80-90% which represent means, but usually from raw small molecules as determinants), Vs. Biologist whom have tables which either use a set distance and angle and little account of variability over time (ie a hydrogen bond equals 1.4 kCal/mol reflecting the absolute mean), conformations in amino acids, etc... I think with gromacs it is very precise, as even the smallest energies between two interacting atoms is taken into account with accuracy reflected by the force fields used, and how they were derived. Good luck, your going to start seeing more and more a flood of biologist. Stephan Watkins Original-Nachricht Datum: Thu, 31 May 2012 19:54:04 +1000 Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond On 31/05/2012 7:46 PM, Acoot Brett wrote: Hi Mark, It is confusing. As you know, for the same hydrogen bond in a protein, the related hydrogen bond angle and bond length can vary within a scope during the whole simulation process, however this small vibration of the hydrogen bond angle and length can lead to significant energy change, and correspondingly the energy of a hydrogen bond in simulation can be varied significantly. In comparison with hydrophobic effect, it would be too much is the energy of the hydrogen bond would be not calculated continuously. It isn't, if the model physics isn't paramtrized to include it explicitly - which is the case for all the force fields in GROMACS. Could you give some further clarification? What are trying to do? Measuring the strength of a hydrogen bond requires you identify a state with and without it and a path between them over which you can integrate. Mark Cheers, Acoot *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, 31 May 2012 4:48 PM *Subject:* Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond On 31/05/2012 4:42 PM, Acoot Brett wrote: Dear All, The value of the energy of the hydrogen bond has relation with distance and angle of the hydrogen bond related atoms. As for in the simulation process, the distance and angle of the hydrogen bond related atoms may change continuously. Will you please let me know based on which formula GROMACS calculated the value of the energy of the hydrogen bonds? There is no such formula used in MD force fields implemented in GROMACS. The only non-bonded
Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond
Dear All, I want to know whether the hydrogen bond energy calculated by the hydrogen bond energy calculation formula alone is higher than the corresponding energy calculated by GROMACS only based on the distance of the key atoms and the charge of the key atoms (of course for hydrogen bond no charge are involved). Cheers, Acoot From: Erik Marklund er...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 3 June 2012 6:18 PM Subject: Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond On the same topic, Espinoza et al. also developed a good estimator for HB energy. See E. Espinosa, E. Molins, C. Lecomte, Chem. Phys. Lett., 285 (1998), p. 170. 31 maj 2012 kl. 16.51 skrev ABEL Stephane 175950: Hi, Here, my 2 cents worth. You can also estimate (roughly !!) the HB energy between two groups (say NH---CO) by using the Kabsch and Sander function described in Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577−2637). Quoting: E = qlq2(1/r(0N) + l/r(CH) - l/r(OH) - l/r(CN))*f with q1 = 0.42e and q 2 = 0.20e, e being the unit electron charge and r(AB) the interatomic distance from A to B. In chemical units, r is in angstroms, the dimensional factor f = 332, and E is in kcal/mol. A good H bond has about -3 kcal/mol binding energy. We choose a generous cutoff to allow for bifurcated H bonds and errors in coordinates and assign an H bond between C=O of residue i and N-H of residue j if E is less than the cutoff, i.e., “Hbond(ij)=: [E -0.5kcal/mole].” To obtain HB energy value E, you need only the distance between the donnor and acceptor groups. HTH Stephane -- Message: 2 Date: Thu, 31 May 2012 15:00:05 +0200 From: lloyd riggs lloyd.ri...@gmx.ch Subject: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 20120531130005.302...@gmx.net Content-Type: text/plain; charset=utf-8 Dear All, I have no clue what specifically you are trying, but I feal bad for all the physicist and quantum chemist whom have provided the software and continued to develop it. Scanning in my free time, it seems a large amount of confusion on what people are trying to do stems from differences in what is taught textbook wise for things. For instance a hydrogen bond to a physicist is an integration over space in 3 dimensions including time and probabilities of occupied spaces (atom position variabilities reflected even more in proteins, ie the necessity of multiple MD runs with different starting conformations), Vs. an organic chemist whom has cut offs, ie angles between two points and set distances between two atoms which generally reflect the means of calculated chemical energies within a range (say 80-90% which represent means, but usually from raw small molecules as determinants), Vs. Biologist whom have tables which either use a set distance and angle and little account of variability over time (ie a hydrogen bond equals 1.4 kCal/mol reflecting the absolute mean), conformations in amino acids, etc... I think with gromacs it is very precise, as even the smallest energies between two interacting atoms is taken into account with accuracy reflected by the force fields used, and how they were derived. Good luck, your going to start seeing more and more a flood of biologist. Stephan Watkins Original-Nachricht Datum: Thu, 31 May 2012 19:54:04 +1000 Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond On 31/05/2012 7:46 PM, Acoot Brett wrote: Hi Mark, It is confusing. As you know, for the same hydrogen bond in a protein, the related hydrogen bond angle and bond length can vary within a scope during the whole simulation process, however this small vibration of the hydrogen bond angle and length can lead to significant energy change, and correspondingly the energy of a hydrogen bond in simulation can be varied significantly. In comparison with hydrophobic effect, it would be too much is the energy of the hydrogen bond would be not calculated continuously. It isn't, if the model physics isn't paramtrized to include it explicitly - which is the case for all the force fields in GROMACS. Could you give some further clarification? What are trying to do? Measuring the strength of a hydrogen bond requires you identify a state with and without it and a path between them over which you can integrate. Mark Cheers, Acoot *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, 31 May 2012 4:48 PM *Subject:* Re: [gmx-users] How GROMACS
Re: [gmx-users] MD Training
I once took this course in Amsterdam and can highly recommend it: http://molsim.chem.uva.nl/molsim2012/index.html 31 maj 2012 kl. 19.44 skrev edward.de...@gmail.com: Dear all, does anyone know of any MD or gromacs training course in the coming months? All the best g- -- Sent from my Nokia phone -- gmx-users mailing listgmx-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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-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
Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond
Hi, Why don't you do the calculations yourself? You have two HB-energy estimators and Gromacs at your disposal. I myself have not verified this, but colleagues have seen a good match between the energy obtained from Espinoza's formula and the populations of HA-distances in simulations. Best, Erik 3 jun 2012 kl. 10.23 skrev Acoot Brett: Dear All, I want to know whether the hydrogen bond energy calculated by the hydrogen bond energy calculation formula alone is higher than the corresponding energy calculated by GROMACS only based on the distance of the key atoms and the charge of the key atoms (of course for hydrogen bond no charge are involved). Cheers, Acoot From: Erik Marklund er...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 3 June 2012 6:18 PM Subject: Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond On the same topic, Espinoza et al. also developed a good estimator for HB energy. See E. Espinosa, E. Molins, C. Lecomte, Chem. Phys. Lett., 285 (1998), p. 170. 31 maj 2012 kl. 16.51 skrev ABEL Stephane 175950: Hi, Here, my 2 cents worth. You can also estimate (roughly !!) the HB energy between two groups (say NH---CO) by using the Kabsch and Sander function described in Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577−2637). Quoting: E = qlq2(1/r(0N) + l/r(CH) - l/r(OH) - l/r(CN))*f with q1 = 0.42e and q 2 = 0.20e, e being the unit electron charge and r(AB) the interatomic distance from A to B. In chemical units, r is in angstroms, the dimensional factor f = 332, and E is in kcal/mol. A good H bond has about -3 kcal/mol binding energy. We choose a generous cutoff to allow for bifurcated H bonds and errors in coordinates and assign an H bond between C=O of residue i and N-H of residue j if E is less than the cutoff, i.e., “Hbond(ij)=: [E -0.5kcal/mole].” To obtain HB energy value E, you need only the distance between the donnor and acceptor groups. HTH Stephane -- Message: 2 Date: Thu, 31 May 2012 15:00:05 +0200 From: lloyd riggs lloyd.ri...@gmx.ch Subject: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 20120531130005.302...@gmx.net Content-Type: text/plain; charset=utf-8 Dear All, I have no clue what specifically you are trying, but I feal bad for all the physicist and quantum chemist whom have provided the software and continued to develop it. Scanning in my free time, it seems a large amount of confusion on what people are trying to do stems from differences in what is taught textbook wise for things. For instance a hydrogen bond to a physicist is an integration over space in 3 dimensions including time and probabilities of occupied spaces (atom position variabilities reflected even more in proteins, ie the necessity of multiple MD runs with different starting conformations), Vs. an organic chemist whom has cut offs, ie angles between two points and set distances between two atoms which generally reflect the means of calculated chemical energies within a range (say 80-90% which represent means, but usually from raw small molecules as determinants), Vs. Biologist whom have tables which either use a set distance and angle and little account of variability over time (ie a hydrogen bond equals 1.4 kCal/mol reflecting the absolute mean), conformations in amino acids, etc... I think with gromacs it is very precise, as even the smallest energies between two interacting atoms is taken into account with accuracy reflected by the force fields used, and how they were derived. Good luck, your going to start seeing more and more a flood of biologist. Stephan Watkins Original-Nachricht Datum: Thu, 31 May 2012 19:54:04 +1000 Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond On 31/05/2012 7:46 PM, Acoot Brett wrote: Hi Mark, It is confusing. As you know, for the same hydrogen bond in a protein, the related hydrogen bond angle and bond length can vary within a scope during the whole simulation process, however this small vibration of the hydrogen bond angle and length can lead to significant energy change, and correspondingly the energy of a hydrogen bond in simulation can be varied significantly. In comparison with hydrophobic effect, it would be too much is the energy of the hydrogen bond would be not calculated continuously. It isn't, if the model physics isn't paramtrized to include it explicitly - which is the case for all the force fields in GROMACS. Could you give some further clarification?
Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond
Thanks. Acoot From: Erik Marklund er...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 3 June 2012 7:03 PM Subject: Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond Hi, Why don't you do the calculations yourself? You have two HB-energy estimators and Gromacs at your disposal. I myself have not verified this, but colleagues have seen a good match between the energy obtained from Espinoza's formula and the populations of HA-distances in simulations. Best, Erik 3 jun 2012 kl. 10.23 skrev Acoot Brett: Dear All, I want to know whether the hydrogen bond energy calculated by the hydrogen bond energy calculation formula alone is higher than the corresponding energy calculated by GROMACS only based on the distance of the key atoms and the charge of the key atoms (of course for hydrogen bond no charge are involved). Cheers, Acoot From: Erik Marklund er...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 3 June 2012 6:18 PM Subject: Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond On the same topic, Espinoza et al. also developed a good estimator for HB energy. See E. Espinosa, E. Molins, C. Lecomte, Chem. Phys. Lett., 285 (1998), p. 170. 31 maj 2012 kl. 16.51 skrev ABEL Stephane 175950: Hi, Here, my 2 cents worth. You can also estimate (roughly !!) the HB energy between two groups (say NH---CO) by using the Kabsch and Sander function described in Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577−2637). Quoting: E = qlq2(1/r(0N) + l/r(CH) - l/r(OH) - l/r(CN))*f with q1 = 0.42e and q 2 = 0.20e, e being the unit electron charge and r(AB) the interatomic distance from A to B. In chemical units, r is in angstroms, the dimensional factor f = 332, and E is in kcal/mol. A good H bond has about -3 kcal/mol binding energy. We choose a generous cutoff to allow for bifurcated H bonds and errors in coordinates and assign an H bond between C=O of residue i and N-H of residue j if E is less than the cutoff, i.e., “Hbond(ij)=: [E -0.5kcal/mole].” To obtain HB energy value E, you need only the distance between the donnor and acceptor groups. HTH Stephane -- Message: 2 Date: Thu, 31 May 2012 15:00:05 +0200 From: lloyd riggs lloyd.ri...@gmx.ch Subject: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 20120531130005.302...@gmx.net Content-Type: text/plain; charset=utf-8 Dear All, I have no clue what specifically you are trying, but I feal bad for all the physicist and quantum chemist whom have provided the software and continued to develop it. Scanning in my free time, it seems a large amount of confusion on what people are trying to do stems from differences in what is taught textbook wise for things. For instance a hydrogen bond to a physicist is an integration over space in 3 dimensions including time and probabilities of occupied spaces (atom position variabilities reflected even more in proteins, ie the necessity of multiple MD runs with different starting conformations), Vs. an organic chemist whom has cut offs, ie angles between two points and set distances between two atoms which generally reflect the means of calculated chemical energies within a range (say 80-90% which represent means, but usually from raw small molecules as determinants), Vs. Biologist whom have tables which either use a set distance and angle and little account of variability over time (ie a hydrogen bond equals 1.4 kCal/mol reflecting the absolute mean), conformations in amino acids, etc... I think with gromacs it is very precise, as even the smallest energies between two interacting atoms is taken into account with accuracy reflected by the force fields used, and how they were derived. Good luck, your going to start seeing more and more a flood of biologist. Stephan Watkins Original-Nachricht Datum: Thu, 31 May 2012 19:54:04 +1000 Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond On 31/05/2012 7:46 PM, Acoot Brett wrote: Hi Mark, It is confusing. As you know, for the same hydrogen bond in a protein, the related hydrogen bond angle and bond length can vary within a scope during the whole simulation process, however this small vibration of the hydrogen bond angle and length can lead to significant energy change, and correspondingly the energy of a hydrogen bond in simulation can be varied significantly. In comparison with hydrophobic effect, it would be too much is the energy of the hydrogen bond would be not calculated continuously. It isn't, if the model physics isn't paramtrized to include it
Re: [gmx-users] MD Training
On Sun, 2012-06-03 at 10:47 +0200, Erik Marklund wrote: I once took this course in Amsterdam and can highly recommend it: http://molsim.chem.uva.nl/molsim2012/index.html Me too. Almost all of the PhD students, who join the group where I am currently working in, go there and so far everbody gave the same good respond response. /Flo 31 maj 2012 kl. 19.44 skrev edward.de...@gmail.com: Dear all, does anyone know of any MD or gromacs training course in the coming months? All the best g- -- Sent from my Nokia phone -- gmx-users mailing listgmx-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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-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 -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-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
[gmx-users] Atomtype 1
Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Thank you! -- gmx-users mailing listgmx-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
Re: [gmx-users] Atomtype 1
On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-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
Re: [gmx-users] Atomtype 1
in fact, the program hang. --- 12年6月3日，周日, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Atomtype 1
in fact, the pdb2gmx still hang. I modified the atomtypes.atp , aminoacids.rtp , ffbonded.itp, ffnonbonded.itp , aminoacids.hdb, residuetypes.dat ,morever, now the pdb2gmx_d even does not the standard protein structure. --- 12年6月3日，周日, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Atomtype 1
On 3/06/2012 11:03 PM, xi zhao wrote: in fact, the pdb2gmx still hang. I modified the atomtypes.atp , aminoacids.rtp , ffbonded.itp, ffnonbonded.itp , aminoacids.hdb, residuetypes.dat4 ,morever, now the pdb2gmx_d even does not the standard protein structure. So clearly you have broken the file format, probably of at least atomtypes.atp. However we can't guess how if we can't see your changes (e.g. use the diff tool). Also, you need to answer the last question Justin asked, because that answer is likely to reveal your problem... Mark --- *12?6?3?,??, Justin A. Lemkul /jalem...@vt.edu/* ??: ???: Justin A. Lemkul jalem...@vt.edu ??: Re: [gmx-users] Atomtype 1 ???: Discussion list for GROMACS users gmx-users@gromacs.org ??: 2012?6?3?,??,??8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://cn.mc151.mail.yahoo.com/mc/compose?to=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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] Atomtype 1
I use Ultraedit to produce new part and paste the files; we add a residue name and corresponding atom type and interaction parameters --- 12年6月3日，周日, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Atomtype 1
On 6/3/12 9:16 AM, xi zhao wrote: I use Ultraedit to produce new part and paste the files; we add a residue name and corresponding atom type and interaction parameters Having never used a commercial text editor, I don't know if its integrity. What happens if you use a different editor, like vi/emacs (Linux/Mac) or Notepad (Windows)? What operating system are you using? The only times I've had pdb2gmx die when reading atom types are when the line endings are bad, so I would strongly suspect this is your issue. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *12年6月3日，周日, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://cn.mc151.mail.yahoo.com/mc/compose?to=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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-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
Re: [gmx-users] Atomtype 1
in windows , I use ultraedit, in linux ,use vi --- 12年6月3日，周日, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午9:19 On 6/3/12 9:16 AM, xi zhao wrote: I use Ultraedit to produce new part and paste the files; we add a residue name and corresponding atom type and interaction parameters Having never used a commercial text editor, I don't know if its integrity. What happens if you use a different editor, like vi/emacs (Linux/Mac) or Notepad (Windows)? What operating system are you using? The only times I've had pdb2gmx die when reading atom types are when the line endings are bad, so I would strongly suspect this is your issue. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *12年6月3日，周日, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://cn.mc151.mail.yahoo.com/mc/compose?to=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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Atomtype 1
On 6/3/12 9:37 AM, xi zhao wrote: in windows , I use ultraedit, in linux ,use vi Does pdb2gmx crash in both cases? If it does, we'll need more information, including what exactly you've done to each file (i.e. show the contents) because there's an outside chance something else may be going wrong. Also, knowing your Gromacs version would be useful as well. I seem to remember a relevant bug a while back that was fixed long ago, so if you're not using 4.5.5, please upgrade and try again. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *12年6月3日，周日, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午9:19 On 6/3/12 9:16 AM, xi zhao wrote: I use Ultraedit to produce new part and paste the files; we add a residue name and corresponding atom type and interaction parameters Having never used a commercial text editor, I don't know if its integrity. What happens if you use a different editor, like vi/emacs (Linux/Mac) or Notepad (Windows)? What operating system are you using? The only times I've had pdb2gmx die when reading atom types are when the line endings are bad, so I would strongly suspect this is your issue. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *12年6月3日，周日, Justin A. Lemkul /jalem...@vt.edu http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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://cn.mc151.mail.yahoo.com/mc/compose?to=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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist
[gmx-users] Re: dangling bond at at one of the terminal ends
HI, everyone am working on a system consisting of protein-DNA complex,where an protein comes and binds to the DNA to form a complex. To produce an topology file in gromacs i gave the command pdb2gmx -f XXX.pdb -o XXX.gro -p XXX.top -ter -ignh -ff amber99 . its creating the topology files of the protein but when its starts creating the topology file for the DNA seq its recognizing the starting and the ending terminus residue. and then stops giving an error Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried editing the .n.tdb and .c.tbd files by writing the terminal residues of DNA in those files but then its giving an error which says need an directive before the residue must been and old file plz help, regards, ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-dangling-bond-at-at-one-of-the-terminal-ends-tp4998029.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: dangling bond at at one of the terminal ends
On 6/3/12 9:47 AM, ramaraju801 wrote: HI, everyone am working on a system consisting of protein-DNA complex,where an protein comes and binds to the DNA to form a complex. To produce an topology file in gromacs i gave the command pdb2gmx -f XXX.pdb -o XXX.gro -p XXX.top -ter -ignh -ff amber99 . its creating the topology files of the protein but when its starts creating the topology file for the DNA seq its recognizing the starting and the ending terminus residue. and then stops giving an error Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried editing the .n.tdb and .c.tbd files by writing the terminal residues of DNA in those files but then its giving an error which says need an directive before the residue must been and old file Editing these files won't actually help, I don't think. The .n.tdb and .c.tdb contain terminal replacement instructions for proteins. For DNA, you should not need them. The error is more indicative of missing atoms. Consult the .rtp entry for your terminal nucleotides - you need to have all the atoms present and named as the force field expects them to be. You can't have anything missing or anything extra. Also, copying and pasting error messages directly from the terminal is vastly more helpful than a description. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-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
[gmx-users] Re: dangling bond at at one of the terminal ends
there were two atoms that were new , i provided them in the .rtp file. only then i ran the command regards ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-dangling-bond-at-at-one-of-the-terminal-ends-tp4998029p4998031.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: dangling bond at at one of the terminal ends
Hi, You may also need to name your terminal DNA residues appropriately in your pdb file, as for the AMBER force fields the terminal DNA residues are named differently. Check out the dna.rtp file for these naming conventions. Cheers Tom On 03/06/12 14:50, Justin A. Lemkul wrote: On 6/3/12 9:47 AM, ramaraju801 wrote: HI, everyone am working on a system consisting of protein-DNA complex,where an protein comes and binds to the DNA to form a complex. To produce an topology file in gromacs i gave the command pdb2gmx -f XXX.pdb -o XXX.gro -p XXX.top -ter -ignh -ff amber99 . its creating the topology files of the protein but when its starts creating the topology file for the DNA seq its recognizing the starting and the ending terminus residue. and then stops giving an error Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file. i tried editing the .n.tdb and .c.tbd files by writing the terminal residues of DNA in those files but then its giving an error which says need an directive before the residue must been and old file Editing these files won't actually help, I don't think. The .n.tdb and .c.tdb contain terminal replacement instructions for proteins. For DNA, you should not need them. The error is more indicative of missing atoms. Consult the .rtp entry for your terminal nucleotides - you need to have all the atoms present and named as the force field expects them to be. You can't have anything missing or anything extra. Also, copying and pasting error messages directly from the terminal is vastly more helpful than a description. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-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
Re: [gmx-users] Atomtype 1
OK, we find the bug. several words have problem of Uppercase and lowercase. thank you very much! --- 12年6月3日，周日, Justin A. Lemkul jalem...@vt.edu 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午9:19 On 6/3/12 9:16 AM, xi zhao wrote: I use Ultraedit to produce new part and paste the files; we add a residue name and corresponding atom type and interaction parameters Having never used a commercial text editor, I don't know if its integrity. What happens if you use a different editor, like vi/emacs (Linux/Mac) or Notepad (Windows)? What operating system are you using? The only times I've had pdb2gmx die when reading atom types are when the line endings are bad, so I would strongly suspect this is your issue. -Justin 4 http://cn.webmessenger.yahoo.com/index.php?t=1to=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *12年6月3日，周日, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: Dear gmx-users: I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d appeared All occupancies are one Opening force field file ./amber99sbr.ff/atomtypes.atp Atomtype 1 Please give me suggestions Did the program hang here? Did it crash? What modifications did you make, and to what files? Are you using a plain text editor that properly treats newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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://cn.mc151.mail.yahoo.com/mc/compose?to=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 http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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 -- gmx-users mailing listgmx-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
[gmx-users] Tabulated potentials for dihedrals - regd
Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Any help please. Thank you in advance. Regards, Ramesh. -- gmx-users mailing listgmx-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
Re: [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?
Dear Chris Thanks again for your reply. On Sat, Jun 2, 2012 at 10:52 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: I suspect that you can find an equation to relate the surface tension to the ratio of the pressure along z to the pressure along xy that is required to maintain the unit cell of a semi-isotropic simulation approximately constant when you use the same compressibility in all dimensions. Actually there is an equation to calculate surface tension by lateral pressure and normal pressure. [image: Inline image 1] 1/2 shows there are two interfaces. Lz is the lenth of box-z. Pn(Z) is normal pressure. Pt(Z) is (press-x + press-y)/2. But pressure must be gotten by correct simulation. You might even find an equation that was based on the rate of unit cell deformation when applying the same pressure in all dimensions. Since this is a non-equilibrium simulation you may need to run many of them to get an average rate. Sorry I don't know how to contact the rate to the surface tension. Or should I use this rate to set my pressure or compressbility? Alternatively, you might consider simulating a spherical glob of decane in a water bath and finding equations that relate the aspherocity to the surface tension. It's interesting and I am thinking about it. It needs a lot of work to do. aha If I were you, I'd look into physics textbooks to find some relation like this that you can use. Chris. -- gmx-users mailing listgmx-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 image.png-- gmx-users mailing listgmx-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
[gmx-users] Regarding error
Dear all gromacs users, While i am running gromacs software i am getting following error.Let me know that error how to over come. Fatal error: There were 22 missing atoms in molecule Protein_chain_A, if you want to use this incomplete topology. Suryanarayana Seera, PhD student, Hyderabad, India. -- gmx-users mailing listgmx-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
