Re: [gmx-users] .top file after using amber2gromacs
On 3/3/14, 12:33 AM, Chetan Mahajan wrote: Thank you, Justin. Could you also tell me if atomtypes section is needed at all? (sample .top file on gromacs website does not have it). If you have additional atom types that are not part of the parent force field, yes, it is necessary. -Justin regards Chetan On Sun, Mar 2, 2014 at 10:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/2/14, 11:24 PM, Chetan Mahajan wrote: Hi All I have gromacs files generated using acpype tool acting on Amber files originally. I need to know the meaning of certain terms in that *.top file (email with attachment of .top file got blocked due to attachment). Unfortunately, I can't find on the web, any material regarding that. It would be great, if anyone could comment on the following. *1. What is the meaning of terms under defaults option at the top of the file (pasted below)?* [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 12 yes 0.5 0.8333 Please refer to manual section 5.7.1, where each of these terms is explained after the urea.top example. * 2a. ** Is atomtypes section needed? (sample .top file on gromacs website does not have it) (pasted after 2b question)**In this atomtypes section, the Amber2gromacs tool keeps mass and charge of each atom as zero. Would a simulation with these places zero be a valid simulation **?* My guess is yes. THis is since, corresponding values are available later in atoms section. The purpose of asking this question is that I have to be sure of the runs I have made, that nothing has gone wrong in having those zeros. Charge and mass information in [atomtypes] is indeed over-written by whatever is found in [atoms]. You can always confirm what has been used by obtaining the grompp-processed topology with grompp -pp or by using gmxdump on the .tpr file. * 2b.I see several enigmatic terms such as bond type p type, Amb. Can you explain these terms, if they are necessary at all? Why last two columns for Amb?* Different force fields work in different ways, so the Gromacs file format is standard across all the different force fields. Since there are generally fewer types of bonded interactions, bonded types are a subset of nonbonded types. Sometimes there are no differences, as is the case here. If a force field uses separate bonded and nonbonded types, that just means the bonded types are an interpretation of the atom types used within ffbonded.itp. The ptype column is particle type - A for atoms, S for shells, V for virtual sites. The last two columns are a comment, likely the original AMBER parameters so you can verify the unit conversion. (part of the data for both 2a and 2b pasted below) [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb Ti Ti 0.0 0.0 A 1.39461e-01 6.08772e-02 ; 0.78 0.0145 OT OT 0.0 0.0 A 2.87832e-01 8.29687e-02 ; 1.62 0.0198 HW HW 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. *4.WHat is cgnr? how is it different from nr? (it appears in atoms section, example below)* cgnr = charge group number nr = atom number -Justin nr type resi res atom cgnr charge mass ; qtot bond_type 1 Ti 1 iO2TI1 1.691002 47.86700 ; qtot 1.691 Thanks -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
[gmx-users] .top file after using amber2gromacs
Hi All I have gromacs files generated using acpype tool acting on Amber files originally. I need to know the meaning of certain terms in that *.top file (email with attachment of .top file got blocked due to attachment). Unfortunately, I can't find on the web, any material regarding that. It would be great, if anyone could comment on the following. *1. What is the meaning of terms under defaults option at the top of the file (pasted below)?* [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 12 yes 0.5 0.8333 * 2a. ** Is atomtypes section needed? (sample .top file on gromacs website does not have it) (pasted after 2b question)**In this atomtypes section, the Amber2gromacs tool keeps mass and charge of each atom as zero. Would a simulation with these places zero be a valid simulation **?* My guess is yes. THis is since, corresponding values are available later in atoms section. The purpose of asking this question is that I have to be sure of the runs I have made, that nothing has gone wrong in having those zeros. * 2b.I see several enigmatic terms such as bond type p type, Amb. Can you explain these terms, if they are necessary at all? Why last two columns for Amb?* (part of the data for both 2a and 2b pasted below) [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb Ti Ti 0.0 0.0 A 1.39461e-01 6.08772e-02 ; 0.78 0.0145 OT OT 0.0 0.0 A 2.87832e-01 8.29687e-02 ; 1.62 0.0198 HW HW 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. *4.WHat is cgnr? how is it different from nr? (it appears in atoms section, example below)* nr type resi res atom cgnr charge mass ; qtot bond_type 1 Ti 1 iO2TI1 1.691002 47.86700 ; qtot 1.691 Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] .top file after using amber2gromacs
On 3/2/14, 11:24 PM, Chetan Mahajan wrote: Hi All I have gromacs files generated using acpype tool acting on Amber files originally. I need to know the meaning of certain terms in that *.top file (email with attachment of .top file got blocked due to attachment). Unfortunately, I can't find on the web, any material regarding that. It would be great, if anyone could comment on the following. *1. What is the meaning of terms under defaults option at the top of the file (pasted below)?* [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 12 yes 0.5 0.8333 Please refer to manual section 5.7.1, where each of these terms is explained after the urea.top example. * 2a. ** Is atomtypes section needed? (sample .top file on gromacs website does not have it) (pasted after 2b question)**In this atomtypes section, the Amber2gromacs tool keeps mass and charge of each atom as zero. Would a simulation with these places zero be a valid simulation **?* My guess is yes. THis is since, corresponding values are available later in atoms section. The purpose of asking this question is that I have to be sure of the runs I have made, that nothing has gone wrong in having those zeros. Charge and mass information in [atomtypes] is indeed over-written by whatever is found in [atoms]. You can always confirm what has been used by obtaining the grompp-processed topology with grompp -pp or by using gmxdump on the .tpr file. * 2b.I see several enigmatic terms such as bond type p type, Amb. Can you explain these terms, if they are necessary at all? Why last two columns for Amb?* Different force fields work in different ways, so the Gromacs file format is standard across all the different force fields. Since there are generally fewer types of bonded interactions, bonded types are a subset of nonbonded types. Sometimes there are no differences, as is the case here. If a force field uses separate bonded and nonbonded types, that just means the bonded types are an interpretation of the atom types used within ffbonded.itp. The ptype column is particle type - A for atoms, S for shells, V for virtual sites. The last two columns are a comment, likely the original AMBER parameters so you can verify the unit conversion. (part of the data for both 2a and 2b pasted below) [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb Ti Ti 0.0 0.0 A 1.39461e-01 6.08772e-02 ; 0.78 0.0145 OT OT 0.0 0.0 A 2.87832e-01 8.29687e-02 ; 1.62 0.0198 HW HW 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. *4.WHat is cgnr? how is it different from nr? (it appears in atoms section, example below)* cgnr = charge group number nr = atom number -Justin nr type resi res atom cgnr charge mass ; qtot bond_type 1 Ti 1 iO2TI1 1.691002 47.86700 ; qtot 1.691 Thanks -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
