Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...
Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- [http://5.cim.co.cu/cim.gif] -- 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] Broken protein chain: WARNING: Listed nonbonded
Note that I am adding position restrains to fix all the termini of the incomplete fragments. Shouldn't that take care of the missing residues? -- Message: 5 Date: Thu, 20 Aug 2015 20:29:42 + From: Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu To: gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: fcd5150195922740996c04d9f8a6dfbb52c4c...@cimex2010mb1.cim.sld.cu Content-Type: text/plain; charset=us-ascii Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? -- Message: 4 Date: Thu, 20 Aug 2015 19:00:29 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: CAMNuMARXoFeT_HN0J57y2pt=gzatnzgb+11asgpm6dxvyq3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- --- [http://5.cim.co.cu/cim.gif] -- Message: 6 Date: Thu, 20 Aug 2015 16:40:27 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: 55d63b3b.6040...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 8/20/15 4:29 PM, Jorge Fernandez de Cossio Diaz wrote: Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? Because you're ignoring something physically relevant - you have missing residues! pdb2gmx certainly gave long bond warnings when you produced the topology. You need to model in the missing residues, otherwise the structure is useless to you. -Justin
Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...
Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? -- Message: 4 Date: Thu, 20 Aug 2015 19:00:29 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: CAMNuMARXoFeT_HN0J57y2pt=gzatnzgb+11asgpm6dxvyq3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- --- [http://5.cim.co.cu/cim.gif] -- 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] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...
On 8/20/15 4:29 PM, Jorge Fernandez de Cossio Diaz wrote: Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? Because you're ignoring something physically relevant - you have missing residues! pdb2gmx certainly gave long bond warnings when you produced the topology. You need to model in the missing residues, otherwise the structure is useless to you. -Justin -- Message: 4 Date: Thu, 20 Aug 2015 19:00:29 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: CAMNuMARXoFeT_HN0J57y2pt=gzatnzgb+11asgpm6dxvyq3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- --- [http://5.cim.co.cu/cim.gif] -- == 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] Broken protein chain: WARNING: Listed nonbonded
On 8/20/15 5:21 PM, Jorge Fernandez de Cossio Diaz wrote: Note that I am adding position restrains to fix all the termini of the incomplete fragments. Shouldn't that take care of the missing residues? If there's a bond between residues that are separated by a large gap, the magnitude of the bonded force is going to be orders of magnitude larger than any restraint force. You need to fix your missing residues. No amount of hacking or trickery is going to give you a sensible result here. -Justin -- Message: 5 Date: Thu, 20 Aug 2015 20:29:42 + From: Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu To: gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: fcd5150195922740996c04d9f8a6dfbb52c4c...@cimex2010mb1.cim.sld.cu Content-Type: text/plain; charset=us-ascii Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction? -- Message: 4 Date: Thu, 20 Aug 2015 19:00:29 + From: Mark Abraham mark.j.abra...@gmail.com To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: CAMNuMARXoFeT_HN0J57y2pt=gzatnzgb+11asgpm6dxvyq3...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues). After trying some things, I realized that if I remove the option -chainsep id from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately. Is there a way to fix the WARNING above without having to remove the option -chainsep id from pdb2gmx? Thanks. Best, cossio --- --- [http://5.cim.co.cu/cim.gif] -- Message: 6 Date: Thu, 20 Aug 2015 16:40:27 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: 55d63b3b.6040...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 8/20/15 4:29 PM, Jorge Fernandez de Cossio Diaz wrote: Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING: WARNING: Listed nonbonded interaction between particles 2897 and 2908 at distance 3f which is larger than the table limit 3f nm. The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space. So why is it that when I put the fragments
