Re: [gmx-users] Energy minimization for Inositol pyrophosphate
On 2/25/15 1:15 AM, ashish bihani wrote: Hello, I have understood my mistakes that I reported in previous queries of this string. now, I am proceeding more systematically. I have generated ff parameters for Inositol Pyrophosphate with the help of PRODRG server (as mentioned in the tutorials) as a residue and added it to Hopefully you're not actually using raw PRODRG parameters, they're generally quite inadequate. aminoacids.rtp. I was able to reformat atoms, bonds, bond angles, dihedrals and impropers by imitating the format of the definitions of other residues. But I am not able to find a format for [ pairs ] which I believe is important for my experiment. Particular pairs defined in ffnonbonded.itp file of gromos54A7 do not have codes unlike dihedrals. If I have two columns for individual atoms (e.g. O35 tab P15 tab ?) involved in the interaction, how do I point the program to corresponding c6 and c12 values in ffnonbonded.itp? The GROMOS force fields only use special pair interactions for certain combinations. If you haven't parametrized these interactions, it's hard to say whether or not you actually need them. Perhaps you should be looking into a more well established force field rather than trying to create one from scratch from a questionable web server. Secondly, the parameter file generated by PRODRG does not contain all the possible dihedral in Inositokl Pyrophosphate. Are those interactions ignored because of some criteria or should I add them manually? You'll have to be more specific about what's missing and why you think it should be there. In general, dihedrals aren't compulsory for every possible bond, but the details vary from force field to force field. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
Re: [gmx-users] Energy minimization for Inositol pyrophosphate
Hello, I have understood my mistakes that I reported in previous queries of this string. now, I am proceeding more systematically. I have generated ff parameters for Inositol Pyrophosphate with the help of PRODRG server (as mentioned in the tutorials) as a residue and added it to aminoacids.rtp. I was able to reformat atoms, bonds, bond angles, dihedrals and impropers by imitating the format of the definitions of other residues. But I am not able to find a format for [ pairs ] which I believe is important for my experiment. Particular pairs defined in ffnonbonded.itp file of gromos54A7 do not have codes unlike dihedrals. If I have two columns for individual atoms (e.g. O35 tab P15 tab ?) involved in the interaction, how do I point the program to corresponding c6 and c12 values in ffnonbonded.itp? Secondly, the parameter file generated by PRODRG does not contain all the possible dihedral in Inositokl Pyrophosphate. Are those interactions ignored because of some criteria or should I add them manually? From: ashish.bih...@outlook.com To: gmx-us...@gromacs.org Subject: RE: Energy minimization for Inositol pyrophosphate Date: Fri, 30 Jan 2015 12:25:43 +0530 Hello, I understand that .itp is a topology file. But the swissparam pack does not have a .gro file. How do I create solvated.gro ? (which has to be used in grompp) Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say whether .itp can sustitute the other two. From: ashish.bih...@outlook.com To: gmx-us...@gromacs.org Subject: Energy minimization for Inositol pyrophosphate Date: Thu, 29 Jan 2015 16:53:56 +0530 Hello all, I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the structure from scratch. I have converted PDB to mol2 with openbabel and submitted at Swissparam (http://swissparam.ch/) which returned a zip file containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, .mol2). 1. Which of these files can be used as force field to generate a topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water spc 2. The regular ffs among the options do not recognize IP7 as its atoms can not be associated with protein/DNA/RNA. All the ffs are based on amino acid residues and nucleotides. Is there an atom based ff available for GROMACS which I can place in ff directory and include in ff list ? (like MMFF)Swissparam help page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 terminology for those atoms. I am having a hard time figuring out what names these atoms should be assigned since all the atoms are unknown. I am attaching the pack returned by swissparam and the version of pdb file with some name modifications.Thank you. -- 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] Energy minimization for Inositol pyrophosphate
On 1/30/15 1:55 AM, ashish bihani wrote: Hello, I understand that .itp is a topology file. But the swissparam pack does not have a .gro file. How do I create solvated.gro ? (which has to be used in grompp) Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say whether .itp can sustitute the other two. Quoting your original message: I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the structure from scratch So you have a coordinate file (.gro format is not mandatory). What's the problem? -Justin From: ashish.bih...@outlook.com To: gmx-us...@gromacs.org Subject: Energy minimization for Inositol pyrophosphate Date: Thu, 29 Jan 2015 16:53:56 +0530 Hello all, I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the structure from scratch. I have converted PDB to mol2 with openbabel and submitted at Swissparam (http://swissparam.ch/) which returned a zip file containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, .mol2). 1. Which of these files can be used as force field to generate a topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water spc 2. The regular ffs among the options do not recognize IP7 as its atoms can not be associated with protein/DNA/RNA. All the ffs are based on amino acid residues and nucleotides. Is there an atom based ff available for GROMACS which I can place in ff directory and include in ff list ? (like MMFF)Swissparam help page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 terminology for those atoms. I am having a hard time figuring out what names these atoms should be assigned since all the atoms are unknown. I am attaching the pack returned by swissparam and the version of pdb file with some name modifications.Thank you. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
[gmx-users] Energy minimization for Inositol pyrophosphate
Hello all, I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the structure from scratch. I have converted PDB to mol2 with openbabel and submitted at Swissparam (http://swissparam.ch/) which returned a zip file containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, .mol2). 1. Which of these files can be used as force field to generate a topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water spc 2. The regular ffs among the options do not recognize IP7 as its atoms can not be associated with protein/DNA/RNA. All the ffs are based on amino acid residues and nucleotides. Is there an atom based ff available for GROMACS which I can place in ff directory and include in ff list ? (like MMFF)Swissparam help page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 terminology for those atoms. I am having a hard time figuring out what names these atoms should be assigned since all the atoms are unknown. I am attaching the pack returned by swissparam and the version of pdb file with some name modifications.Thank you. -- 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] Energy minimization for Inositol pyrophosphate
On 1/29/15 6:23 AM, ashish bihani wrote: Hello all, I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the structure from scratch. I have converted PDB to mol2 with openbabel and submitted at Swissparam (http://swissparam.ch/) which returned a zip file containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, .mol2). 1. Which of these files can be used as force field to generate a topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water spc 2. The regular ffs among the options do not recognize IP7 as its atoms can not be associated with protein/DNA/RNA. All the ffs are based on amino acid residues and nucleotides. Is there an atom based ff available for GROMACS which I can place in ff directory and include in ff list ? (like MMFF)Swissparam help page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 terminology for those atoms. I am having a hard time figuring out what names these atoms should be assigned since all the atoms are unknown. I am attaching the pack returned by swissparam and the version of pdb file with some name modifications.Thank you. If you have an .itp file, that's a topology. You don't need to run through pdb2gmx again, because the purpose of pdb2gmx is to create a topology. If file formats are unfamiliar to you, refer to Chapter 5 of the manual where all of this is covered. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
Re: [gmx-users] Energy minimization for Inositol pyrophosphate
Hello, I understand that .itp is a topology file. But the swissparam pack does not have a .gro file. How do I create solvated.gro ? (which has to be used in grompp) Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say whether .itp can sustitute the other two. From: ashish.bih...@outlook.com To: gmx-us...@gromacs.org Subject: Energy minimization for Inositol pyrophosphate Date: Thu, 29 Jan 2015 16:53:56 +0530 Hello all, I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the structure from scratch. I have converted PDB to mol2 with openbabel and submitted at Swissparam (http://swissparam.ch/) which returned a zip file containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, .mol2). 1. Which of these files can be used as force field to generate a topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water spc 2. The regular ffs among the options do not recognize IP7 as its atoms can not be associated with protein/DNA/RNA. All the ffs are based on amino acid residues and nucleotides. Is there an atom based ff available for GROMACS which I can place in ff directory and include in ff list ? (like MMFF)Swissparam help page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 terminology for those atoms. I am having a hard time figuring out what names these atoms should be assigned since all the atoms are unknown. I am attaching the pack returned by swissparam and the version of pdb file with some name modifications.Thank you. -- 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.
