[gmx-users] Grompp error No default Ryckaert-Bell. types
Hello all How can I address the No default Ryckaert-Bell. types error. The error is also in between the atoms which are not bonded with each other. Thank you -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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] Grompp error No default Ryckaert-Bell. types
You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever. Alex Thank you for your reply. I am simulating a PLGA (poly lactic co-glycolic acid molecle). I get the topology file and I solvated the molecule. my system is neutral. while running the grompp I got 6 No default Ryckaert-Bell. types. I rechecked my parameters in .rtp file and I found them correct, or may be I am unable to found the problem. I am using ions.mdp file which is given in the tutorial (lysozyme tutorial). I have attatched the .pdb file and the .rtp parameters for them. can you please check the parameters which I have given. so that I can rectify the errors. awaiting for your reply. Best Anurag Dobhal Juniour Research fellow Supervisor: Dr. Ratnesh D. Jain Department of chemical engineering Insttute of Chemical Technology 400019, +91 8898486877 On Mon, May 4, 2015 at 12:11 PM, Alex nedoma...@gmail.com wrote: It may sound surprising, but this is resolved by either introducing correct R-B term parameters in your topology/ff definitions, or by removing the mess from the input coordinates, especially when non-bonded atoms are determined to participate in a dihedral. Humor aside, more information about the system is needed. Alex AD Hello all AD How can I address the "No default Ryckaert-Bell. types error". AD The error is also in between the atoms which are not bonded with each other. AD Thank you AD -- AD *DISCLAIMER:* AD *This communication is intended only for the person or entity to which it AD is addressed and may contain confidential and / or privileged material. Any AD review, retransmission, dissemination or other use is prohibited. If you AD have received this in error, please contact the sender and delete this AD material from your computer. Kindly note that this mail does not constitute AD an offer or solicitation for the purchase or sale of any financial AD instrument or as an official confirmation of any transaction. The AD information is not warranted as to completeness or accuracy and is subject AD to change without notice. Any comments or statements made herein do not AD necessarily reflect those of Nanomedicine Research Group. Before opening AD the email or accessing any attachments, please check and scan for virus.* DISCLAIMER: This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus. -- Best regards, Sasha mailto:nedoma...@gmail.com -- 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] Grompp error No default Ryckaert-Bell. types
"Which angles?" -- wait until Mark Abraham gets here. You must have a very special version of aminoacids.rtp Example: https://github.com/gromacs/gromacs/blob/master/share/top/gromos43a2.ff/aminoacids.rtp Thank you But which angles I need to add in .rtp file. are you talking about impropers and dihedrals ??? as In aminoacid.rtp there is no section for angles. Best Anurag Dobhal Juniour Research fellow Supervisor: Dr. Ratnesh D. Jain Department of chemical engineering Insttute of Chemical Technology 400019, +91 8898486877 On Mon, May 4, 2015 at 12:47 PM, Sasha nedoma...@gmail.com wrote: You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever. Alex Thank you for your reply. I am simulating a PLGA (poly lactic co-glycolic acid molecle). I get the topology file and I solvated the molecule. my system is neutral. while running the grompp I got 6 No default Ryckaert-Bell. types. I rechecked my parameters in .rtp file and I found them correct, or may be I am unable to found the problem. I am using ions.mdp file which is given in the tutorial (lysozyme tutorial). I have attatched the .pdb file and the .rtp parameters for them. can you please check the parameters which I have given. so that I can rectify the errors. awaiting for your reply. Best Anurag Dobhal Juniour Research fellow Supervisor: Dr. Ratnesh D. Jain Department of chemical engineering Insttute of Chemical Technology 400019, +91 8898486877 On Mon, May 4, 2015 at 12:11 PM, Alex nedoma...@gmail.com wrote: It may sound surprising, but this is resolved by either introducing correct R-B term parameters in your topology/ff definitions, or by removing the mess from the input coordinates, especially when non-bonded atoms are determined to participate in a dihedral. Humor aside, more information about the system is needed. Alex AD Hello all AD How can I address the "No default Ryckaert-Bell. types error". AD The error is also in between the atoms which are not bonded with each other. AD Thank you AD -- AD *DISCLAIMER:* AD *This communication is intended only for the person or entity to which it AD is addressed and may contain confidential and / or privileged material. Any AD review, retransmission, dissemination or other use is prohibited. If you AD have received this in error, please contact the sender and delete this AD material from your computer. Kindly note that this mail does not constitute AD an offer or solicitation for the purchase or sale of any financial AD instrument or as an official confirmation of any transaction. The AD information is not warranted as to completeness or accuracy and is subject AD to change without notice. Any comments or statements made herein do not AD necessarily reflect those of Nanomedicine Research Group. Before opening AD the email or accessing any attachments, please check and scan for virus.* DISCLAIMER: This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus. -- Best regards, Sasha mailto:nedoma...@gmail.com DISCLAIMER: This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus. -- Best regards, Alex mailto:nedoma...@gmail.com -- 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
Re: [gmx-users] Grompp error No default Ryckaert-Bell. types
The rtp file format and its acceptable entries are not forcefield-specific (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to give an example of that. The oplsaa version of aminoacids.rtp only lists dihedral and improper angles explicitly, and that is exactly what's grompp complaining about in your case. Alex Dear Sir I am using oplsaa force field. In the .rtp file i did not found angles secion for any amino acid. yes there are sections for dihedrals and impropers. sorry for troubling you. Best Anurag Dobhal Juniour Research fellow Supervisor: Dr. Ratnesh D. Jain Department of chemical engineering Insttute of Chemical Technology 400019, +91 8898486877 On Mon, May 4, 2015 at 1:03 PM, Alex nedoma...@gmail.com wrote: "Which angles?" -- wait until Mark Abraham gets here. You must have a very special version of aminoacids.rtp Example:https://github.com/gromacs/gromacs/blob/master/share/top/gromos43a2.ff/aminoacids.rtp Thank you But which angles I need to add in .rtp file. are you talking about impropers and dihedrals ??? as In aminoacid.rtp there is no section for angles. Best Anurag Dobhal Juniour Research fellow Supervisor: Dr. Ratnesh D. Jain Department of chemical engineering Insttute of Chemical Technology 400019, +91 8898486877 On Mon, May 4, 2015 at 12:47 PM, Sasha nedoma...@gmail.com wrote: You said you found the rtp entry to be correct, and yet the one you attached has no angles listed, none whatsoever. Alex Thank you for your reply. I am simulating a PLGA (poly lactic co-glycolic acid molecle). I get the topology file and I solvated the molecule. my system is neutral. while running the grompp I got 6 No default Ryckaert-Bell. types. I rechecked my parameters in .rtp file and I found them correct, or may be I am unable to found the problem. I am using ions.mdp file which is given in the tutorial (lysozyme tutorial). I have attatched the .pdb file and the .rtp parameters for them. can you please check the parameters which I have given. so that I can rectify the errors. awaiting for your reply. Best Anurag Dobhal Juniour Research fellow Supervisor: Dr. Ratnesh D. Jain Department of chemical engineering Insttute of Chemical Technology 400019, +91 8898486877 On Mon, May 4, 2015 at 12:11 PM, Alex nedoma...@gmail.com wrote: It may sound surprising, but this is resolved by either introducing correct R-B term parameters in your topology/ff definitions, or by removing the mess from the input coordinates, especially when non-bonded atoms are determined to participate in a dihedral. Humor aside, more information about the system is needed. Alex AD Hello all AD How can I address the "No default Ryckaert-Bell. types error". AD The error is also in between the atoms which are not bonded with each other. AD Thank you AD -- AD *DISCLAIMER:* AD *This communication is intended only for the person or entity to which it AD is addressed and may contain confidential and / or privileged material. Any AD review, retransmission, dissemination or other use is prohibited. If you AD have received this in error, please contact the sender and delete this AD material from your computer. Kindly note that this mail does not constitute AD an offer or solicitation for the purchase or sale of any financial AD instrument or as an official confirmation of any transaction. The AD information is not warranted as to completeness or accuracy and is subject AD to change without notice. Any comments or statements made herein do not AD necessarily reflect those of Nanomedicine Research Group. Before opening AD the email or accessing any attachments, please check and scan for virus.* DISCLAIMER: This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. The information is not warranted as to completeness or accuracy and is subject to change without notice. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus. -- Best regards, Sasha mailto:nedoma...@gmail.com DISCLAIMER: This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Kindly note that this mail does not constitute an offer or
Re: [gmx-users] Grompp error No default Ryckaert-Bell. types
On 5/4/15 4:20 AM, Alex wrote: The rtp file format and its acceptable entries are not forcefield-specific (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to give an example of that. The oplsaa version of aminoacids.rtp only lists dihedral and improper angles explicitly, and that is exactly what's grompp complaining about in your case. I seem to be only getting half of the messages in this conversation, but let me clear a few things up: 1. The errors about missing R-B parameters have nothing to do with missing angles in the .rtp. R-B are dihedrals, so that's not what grompp is complaining about. 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are required to define connectivity. Remaining bonded interactions are then deduced from bond connectivity. If a directive like [angles] or [dihedrals] is present, those values are used, instead. If an [angles] directive is missing that just tells pdb2gmx create all possible angles from the given bonded connectivity. -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] atom freezing during simulation
On 5/4/15 1:10 AM, mah maz wrote: Hi Justin, Unfortunately, I am looking at the right atoms! Coordinates of the frozen atoms are different from their initial ones and they have non-zero velocities. I set up the .mdp file as follows: freezegrps = frz1 frz2 freezdim = x y z x y z Is it the correct way of setting up frozen groups? No. Valid options are Y (yes) or N (no) for each dimension. See http://manual.gromacs.org/online/mdp_opt.html#neq In your case, you're freezing along the y-axis only. -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] Justin biphasic tutorial with controlled adsoption of protein
On 5/3/15 10:29 PM, James Lord wrote: Hi Justin, I definitely saw this in the manual but as I said before couldn't get the part a suitable [position_restraints] and negative force constant in your earlier email. Would you please let me know the right way of doing this? may be an example of the command etc to be used? It's not a command, it's a topology directive. You'll have to play with it a bit yourself; I don't have time to create and test an example to do what you want. Do something simple, like one particle in a small box, something that is easily tested and verified, before moving to your complex system. -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] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4
Can you walk me through that image and tell me what you see that is different from what you expect? I see a maximum at z=0 in both cases (I presume z=0 is the bilayer center). I'm happy to continue guessing, but you are really best to take something like hexane in a simplified bilayer and do a test. If you don't see something like this: http://pubs.acs.org/doi/abs/10.1021/ja0535099 then you've got a problem. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of mahender singh pharmbioc...@live.com Sent: 04 May 2015 00:57 To: gromacs user_list Subject: Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4 Thanks Chris for your help I am using Isoniazid drug and the membrane model is a mixture of different lipid types (POPE,POPC,POPI,POPS,cholesterol) in a ratio mimicking the plasma membrane more closely as compared to the simple single lipid type membrane model. I have attached the PMF plot (attachment, shared link), and sorry for the partial PMF graph as one can see sampling is not sufficient , as I stopped further umbrella sampling, because of strange results. One is made by using pull-geometry=distance, free, energy on the negative side (limited to the one leaflet, as distance between two group become zero drug will not move onto the other side) and other by using pull-geometry=direction for the same drug i.e. isoniazid, free energy on the positive side. https://onedrive.live.com/redir?resid=DA38458F80BE68E9!192authkey=!ACGecvNH6tPzIloithint=folder%2c All the parameters were same except pull-geomerty i.e distance or direction. But free energy graph is completely opposite in both the cases and this should not be , as I thinks. As for the same drug free energy profile should not be completely opposite for the one drug, so may be I making some mistake in the umbrella sampling parameters. Can you provide me some suggestion on this topic. Thanks in advance for help. with regards Mahender Singh Hello good morning to all I did steered md simulation by using following code ;pull code pull= umbrella pull_geometry= direction pull_dim= N N Y pull_coord1_vec=0 0 1 pull_start= yes pull_ngroups=2 pull-ncoords=1 pull_coord1_groups= 1 2 pull_group1_name= NPROT_ref pull_group2_name= LIG pull_coord1_rate= 0.004; 0.004 nm per ps = 4 nm per ns pull_coord1_k= 1000; kJ mol^-1 nm^-2 pull_nstxout= 500; every 1 ps pull_nstfout= 500; every 1 ps And then used these results of SMD for umbrella sampling (total umbrella window =30 across the membrane) by using following code pull= umbrella pull_geometry= direction pull_dim= N N Y pull_coord1_vec=0 0 1 pull_start= yes pull_ngroups=2 pull-ncoords=1 pull_coord1_groups= 1 2 pull_group1_name= NPROT_ref pull_group2_name= LIG pull_coord1_rate= 0.0 pull_coord1_k= 1000; kJ mol^-1 nm^-2 pull_nstxout= 500; every 1 ps pull_nstfout= 500; every 1 ps In my case, I am moving a molecule from -z to +z across the membrane. So I used pull-geometry=direction in gromacs 5.0.4 (as per gromacs site= http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force), as I cannot use pull-geimetry=distance. Every thing completed correctly (seems to me), but when I used gmx wham on the pullf.xvg files, PMF profile was on the positive side. PMF increased from 0 (bulk water) to 60 at the center of the membrane and than again decreased to the 0 (bulk water on the other side). I all the literature, PMF values for the molecule crossing a membrane is on the negative side and minimum at the center. I am confused about the result. Did I do something wrong with the parameters or understanding the PMF curve wrongly. can any one give their suggestion on this. thanks in advance of user time and help. with regards Mahender Singh -- 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. -- Message: 3 Date: Sun, 3 May 2015 12:25:01 + From: Christopher Neale chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4 Message-ID: 1430655898617.32...@alum.utoronto.ca Content-Type: text/plain; charset=iso-8859-1 Better yet, repeat something that is already out there in the literature.
Re: [gmx-users] Grompp error No default Ryckaert-Bell. types
JL 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are JL required to define connectivity. Remaining bonded interactions are then deduced JL from bond connectivity. If a directive like [angles] or [dihedrals] is present, JL those values are used, instead. If an [angles] directive is missing that just JL tells pdb2gmx create all possible angles from the given bonded connectivity. Well, yes, but the atomtypes were defined in that rtp and no correct triplets or quadruplets were available in ffbonded for those combinations. Then, either define directly in rtp, or stick them into your ffbonded. Am I missing something here? Alex -- 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] Grompp error No default Ryckaert-Bell. types
On 5/4/15 1:06 PM, Alex wrote: JL 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are JL required to define connectivity. Remaining bonded interactions are then deduced JL from bond connectivity. If a directive like [angles] or [dihedrals] is present, JL those values are used, instead. If an [angles] directive is missing that just JL tells pdb2gmx create all possible angles from the given bonded connectivity. Well, yes, but the atomtypes were defined in that rtp and no correct triplets or quadruplets were available in ffbonded for those combinations. Then, either define directly in rtp, or stick them into your ffbonded. Am I missing something here? I was just clarifying what was a very (to me) confusing exchange. The statements made could easily be taken out of context and misapplied. oplsaa seems to look up triplets for [ angles ] elsewhere is not really right, that's what I was explaining about the fundamental way pdb2gmx processes the .rtp to write angles and dihedrals. The oplsaa version of aminoacids.rtp only lists dihedral and improper angles explicitly, and that is exactly what's grompp complaining about in your case. As worded, this seems like you're saying that the fact that only dihedrals and impropers are listed is the source of the problem. That's not the case, but what you say above is - the parameters for the defined interaction are simply not in the force field and therefore must be added. Of course, if the OP had simply Googled the error, this information would have been readily apparent and would have saved all involved a lot of typing :) -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] Grompp error No default Ryckaert-Bell. types
True, thats why i mentioned Mark.:-) In all honesty, though, for small molecules, i would prefer to ignore the new format and actually add everything in the rtp entry to make ffbonded look like less of a zoo. Also, it was late night of extreme gromacs intercourse for me, which finally paid off. :-) Alex On May 4, 2015 11:31 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/4/15 1:06 PM, Alex wrote: JL 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are JL required to define connectivity. Remaining bonded interactions are then deduced JL from bond connectivity. If a directive like [angles] or [dihedrals] is present, JL those values are used, instead. If an [angles] directive is missing that just JL tells pdb2gmx create all possible angles from the given bonded connectivity. Well, yes, but the atomtypes were defined in that rtp and no correct triplets or quadruplets were available in ffbonded for those combinations. Then, either define directly in rtp, or stick them into your ffbonded. Am I missing something here? I was just clarifying what was a very (to me) confusing exchange. The statements made could easily be taken out of context and misapplied. oplsaa seems to look up triplets for [ angles ] elsewhere is not really right, that's what I was explaining about the fundamental way pdb2gmx processes the .rtp to write angles and dihedrals. The oplsaa version of aminoacids.rtp only lists dihedral and improper angles explicitly, and that is exactly what's grompp complaining about in your case. As worded, this seems like you're saying that the fact that only dihedrals and impropers are listed is the source of the problem. That's not the case, but what you say above is - the parameters for the defined interaction are simply not in the force field and therefore must be added. Of course, if the OP had simply Googled the error, this information would have been readily apparent and would have saved all involved a lot of typing :) -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. -- 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] CHARMM36 Termini Topology Incomplete
On 5/4/15 4:09 PM, Jarrett Lee Wise wrote: I had similar problems when I was making polymers. You have to input those parameters directly or delete those lines in the itp/topology file depending if they are important or not. The correct way would be to do quantum I don't know how one decides whether a parameter is important or not, but in general it's very dangerous to simply make ad hoc deletions. There should not be missing terms, though it is entirely possible that a dihedral will have an amplitude of zero (e.g. the normal nonbonded parameters result in a correct 1-D energy scan), in which case the deletion is OK. But this is rare. Bonds and angles should certainly not be deleted because of missing parameters. -Justin calculations for the missing parameters, but I inserted similar ones for the missing ones e.g. CH2 parameter for a CH1 parameter. Jarrett Wise -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of João Rodrigues Sent: Monday, May 04, 2015 1:44 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] CHARMM36 Termini Topology Incomplete Hi all, I am trying to setup a simulation of a peptide with neutral termini, using the CHARMM36 port from the MacKerell lab. While pdb2gmx works well, grompp fails with several erros about missing parameters, e.g.: ERROR 1 [file topol.top, line 1225]: No default U-B types ... ERROR 4 [file topol.top, line 1689]: No default Proper Dih. types All these are related to the termini, whether I use CT2 or COOH, or NH2. Could I copy the missing parameters from the old CHARMM27.ff files? Or should I contact the developers directly? The default charged termini work fine. Or should I add the ACE/NMA caps in f.e. Pymol? Cheers, João -- 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 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.
