[gmx-users] sampling the side chain conformations by MD simulations
Dear All: I am conducting molecular dynamics simulations of a proetin. The side chain conformation of one key residue is important for the protein function and I wang to sampling its conformations and calculate the energy barrier when it changes between different conformations. However, the common MD simulations can't sampling all of its conformations (maybe the energy barrier between different conformations is high?) and I want to enhance the sampling process. My question is does it possible to use high temperature for this residue and normal temperature for the other part of the system so that I can sample more conformations in relative short time? I know locally enhanced sampling method maybe useful in this situation, but it seemed that it is not implemented in the GMX package. I will be appraciate if anyone could give me some suggestions. RXG -- 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] PDB2GMX error in charmm27 Forcefield
Hi all, Im using Charmm27 Forcefield to generate topology of my protein by using PDB2GMX tool but is showing Fatal Error Atom OG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 178. Can any body tell me how to solve this... Regards, -- Sainitin D -- 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] PDB2GMX error in charmm27 Forcefield
On 22/04/2012 10:58 PM, sai nitin wrote: Hi all, Im using Charmm27 Forcefield to generate topology of my protein by using PDB2GMX tool but is showing Fatal Error Atom OG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 178. Can any body tell me how to solve this... No. We don't know your pdb2gmx command line or what is in your system or what is happening at residue 178. Mark -- 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] PDB2GMX error in charmm27 Forcefield
On 2012-04-22 17:11, Mark Abraham wrote: On 22/04/2012 10:58 PM, sai nitin wrote: Hi all, Im using Charmm27 Forcefield to generate topology of my protein by using PDB2GMX tool but is showing Fatal Error Atom OG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 178. Can any body tell me how to solve this... No. We don't know your pdb2gmx command line or what is in your system or what is happening at residue 178. Mark more likely your protein is missing a side chain. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] File editing - only one layer of water around a molecule
Hi Justin You wrote: If you do not specify any output file, the default is this .xvg file that tells you how many atoms satisfied the criterion specified in the selection string. If you want a coordinate file, it's a two-step process. 1. Run g_select using the -on flag to produce an output index file of the atoms that satisfy your criterion. 2. Use trjconv with that index file in and your coordinate file to generate the structure with those atoms. I used the command: g_select -s molecule_in_water.pdb -select 'Close to ISO resname SOL and within 0.5 of resname ISO' -on And got the size.xvg file and an index.ndx file. Than I want to make my coordinate file by trjconv -n index.ndx and got the error Can not open file: traj.xtc I have no traj.xtc file. Thank you for helping me Greetings Lara Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org Gesendet: 17:27 Samstag, 14.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule Lara Bunte wrote: Hi Justin The difference in my g_select -s molecule_in_water.pdb -select 'Close to ISO resname SOL and within 0.5 of group ISO' and your g_select -s molecule_in_water.pdb -select 'Close to ISO resname SOL and within 0.5 of resname ISO' is, that the last ISO is not in quotation marks. Could you please explain? There is a much greater difference. The first command uses 'group ISO' which assumes that there is a group (either generated by default or present in a supplied index file) named ISO. Apparently this is not the case. What I used was 'resname ISO' which is generic syntax for any residue name that I like (i.e., not a group). You can use it with any residue name in the structure. With your command I got this time no error but I got other stuff that I don't understand: 1.) I got this warnings: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. WARNING: if there are broken molecules in the trajectory file, they can not be made whole without a run input file Can I ignore this or is this serious? These are probably not important. They are generic warnings that many Gromacs programs will produce if they are run without a .tpr file. 2.) My output is one file called size.xvg. It contains # This file was created Sat Apr 14 16:55:56 2012 # by the following command: # g_select -s molecule_in_water.pdb -select Close to ISO resname SOL and within 0.5 of resname ISO # # g_select is part of G R O M A C S: # # Green Red Orange Magenta Azure Cyan Skyblue # @ title Selection size @ xaxis label Time (ps) @ yaxis label Number @TYPE xy # Selections: # Close to ISO resname SOL and within 0.5 of resname ISO # @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Close to ISO 0.000 848.000 What is the interpretation of this? What I need is a new pdb. file that has to contain only the molecule ISO and the water layer SOL around it. Is this possible with g_select? If you do not specify any output file, the default is this .xvg file that tells you how many atoms satisfied the criterion specified in the selection string. If you want a coordinate file, it's a two-step process. 1. Run g_select using the -on flag to produce an output index file of the atoms that satisfy your criterion. 2. Use trjconv with that index file in and your coordinate file to generate the structure with those atoms. -Justin Thanks for helping me. Greetings Lara p.s. I use yahoo. I tried to find an answer to all option or something like that. Again after pressing answer the mail should go only to Justin. I put the mailing list in cc. Is here someone using yahoo also and know how to fix this? *Von:* Justin A. Lemkul jalem...@vt.edu *An:* Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org *Gesendet:* 16:56 Samstag, 14.April 2012 *Betreff:* Re: [gmx-users] File editing - only one layer of water around a molecule Lara Bunte wrote: I still got the problem. What is wrong in this command: g_select -s molecule_in_water.pdb -select 'Close to ISO resname SOL and within 0.5 of group ISO' In the pdb. file ISO is for the molecule and SOL for the water. Please help The above command assumes ISO is a default group, like Protein or something else. You can make selections based on any arbitrary residue name with something like the following: g_select -s molecule_in_water.pdb -select 'Close to ISO resname SOL and within 0.5 of resname ISO' Does that work?
Re: [gmx-users] File editing - only one layer of water around a molecule
On 4/22/12 3:55 PM, Lara Bunte wrote: Hi Justin You wrote: If you do not specify any output file, the default is this .xvg file that tells you how many atoms satisfied the criterion specified in the selection string. If you want a coordinate file, it's a two-step process. 1. Run g_select using the -on flag to produce an output index file of the atoms that satisfy your criterion. 2. Use trjconv with that index file in and your coordinate file to generate the structure with those atoms. I used the command: g_select -s molecule_in_water.pdb -select 'Close to ISO resname SOL and within 0.5 of resname ISO' -on And got the size.xvg file and an index.ndx file. Than I want to make my coordinate file by trjconv -n index.ndx and got the error Can not open file: traj.xtc I have no traj.xtc file. If you do not specify any other options, trjconv (like all Gromacs programs) searches for default file names (listed in the manual and/or the help information printed with -h). You need to provide explicit file names for -s and -f in this case, and perhaps -o to choose an appropriate file name and format if for some reason you do not wish to use the default name. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] File editing - only one layer of water around a molecule
Hi I got always the same error. I tried trjconv -n index.ndx -s molecule_in_water.pdb -o output Could you please send an example command how to get the coordinate file out of my index file? I typed trjconv -h but I can't filter the knowledge out, thats to much for me. Thanks for helping Greetings Lara Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org Gesendet: 22:37 Sonntag, 22.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/22/12 3:55 PM, Lara Bunte wrote: Hi Justin You wrote: If you do not specify any output file, the default is this .xvg file that tells you how many atoms satisfied the criterion specified in the selection string. If you want a coordinate file, it's a two-step process. 1. Run g_select using the -on flag to produce an output index file of the atoms that satisfy your criterion. 2. Use trjconv with that index file in and your coordinate file to generate the structure with those atoms. I used the command: g_select -s molecule_in_water.pdb -select 'Close to ISO resname SOL and within 0.5 of resname ISO' -on And got the size.xvg file and an index.ndx file. Than I want to make my coordinate file by trjconv -n index.ndx and got the error Can not open file: traj.xtc I have no traj.xtc file. If you do not specify any other options, trjconv (like all Gromacs programs) searches for default file names (listed in the manual and/or the help information printed with -h). You need to provide explicit file names for -s and -f in this case, and perhaps -o to choose an appropriate file name and format if for some reason you do not wish to use the default name. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] File editing - only one layer of water around a molecule
On 4/22/12 5:07 PM, Lara Bunte wrote: Hi I got always the same error. I tried trjconv -n index.ndx -s molecule_in_water.pdb -o output Could you please send an example command how to get the coordinate file out of my index file? I typed trjconv -h but I can't filter the knowledge out, thats to much for me. You should be passing your coordinate file to -f, not -s. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Radial distribution function (RDF) in cylindrical coordinates
Hi, I have a system that is effectively two-dimensional. I have two parallel plates, which are each parallel to the xy plane. Thus, I have what I think one would call slab geometry. Since my system is clearly not isotropic, it does not make sense to compute radial distribution functions in the standard way (i.e., considering a sphere around the atom/molecule of interest). Do you know if it is possible to compute radial distribution functions in cylindrical coordinates? In the documentation for g_rdf, there is a switch -[no]xy which by default is set to no. This switch is described as Use only the x and y components of the distance. Am I correct in understanding that -xy is effectively computing the RDF in cylindrical coordinates? I guess this would mean that, for every atom/molecule of interest, you would consider a cylinder whose axis is parallel to the z axis (and the z axis is perpendicular to the plates, which are parallel to the xy plane). Basically, my question is the same as that asked here: http://lists.gromacs.org/pipermail/gmx-users/2009-April/041475.html , although it doesn't seem that that post was resolved. Thank you! Andrew DeYoung Carnegie Mellon University -- 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] Radial distribution function (RDF) in cylindrical coordinates
On 4/22/12 5:39 PM, Andrew DeYoung wrote: Hi, I have a system that is effectively two-dimensional. I have two parallel plates, which are each parallel to the xy plane. Thus, I have what I think one would call slab geometry. Since my system is clearly not isotropic, it does not make sense to compute radial distribution functions in the standard way (i.e., considering a sphere around the atom/molecule of interest). Do you know if it is possible to compute radial distribution functions in cylindrical coordinates? In the documentation for g_rdf, there is a switch -[no]xy which by default is set to no. This switch is described as Use only the x and y components of the distance. Am I correct in understanding that -xy is effectively computing the RDF in cylindrical coordinates? I guess this would mean that, for every atom/molecule of interest, you would consider a cylinder whose axis is parallel to the z axis (and the z axis is perpendicular to the plates, which are parallel to the xy plane). When the -xy option is enabled, PBC is turned off in the z-dimension and distances are computed from the x- and y-components only. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] g_rdf -surf -rdf res_com: details needed
Hello,
I wish to compute rdf of Na+ ions around protein surface. I use the command:
g_rdf -f traj.xtc -n index.ndx -o rdf_prot_Na_res_com.xvg -b 4 -s md.tpr
-surf mol -rdf res_com -bin 0.01
Since when -surf option is used, g_rdf does not normalize the rdf, I am
curious what does actually g_rdf reports in the output .xvg file? If we
refer to the Eq. (8.3) of gromacs_manual.pdf, which of the following value
gets reported in the output file:
1) \sum_{1,N_B} (\delta(r_{i,j}-r))
2) \sum_{1,N_B} (\delta(r_{i,j}-r)) / (4*pi*r^2)
3) \sum_{1,N_B} (\delta(r_{i,j}-r)) / (4*pi*r^2) / N_A
My hunch is that g_rdf -surf reports value calculated by Eq. 1 since
computing the term (4*pi*r^2) for an irregular surface is very complex.
Please advise ?
My second question is regarding the value of r_max. In the manual, it's
reported: Usually the value of rmax is half of the box length. When I
compute rdf using g_rdf -surf option, the value of maximum r is indeed half
the box length. However, I think the value of r_max, when -surf is used,
should be considerably less than the (box length)/2. If I am right, in this
case, r is the distance from the surface of the protein and not from the
center of the protein. Hence, r_max should be around the length of solvent
padding from protein surface.
Thanks,
Neeraj
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Re: [gmx-users] Heme group with CHARMM27 FF
Dear Abraham, Sorry for making it hard. Since I am so new to this I guess I am not explaining it clearly for you to help me. First of all I dont want to ignore any hydrogens but as pdb2gmx was complaining about my system and suggested me to add -ignh I did so. My problem is how to update .hdb with heme hydrogen details. So, here to follow your suggestion removing the hydrogen atoms I wish to ignore I actually need to ignore the hydorgens in protein. Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 8:08 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 9:02 PM, Sundar Jubilant wrote: Dear Abraham, How would it work if I remove the hydrogen atoms that I wish to ignore from my input co-ordinate file? The pdb2gmx tries to add the missing hydorgen atoms for which the .hdb doesn't have information. You've never actually told us what hydrogens you want to ignore, so you're making it hard to help you. Mark In my case here, I can consider heme as a ligand instead of having it as protein since it doesn't need to be the part of the protein. Thanks for your information. Sundar -OriginalMessage- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 6:42 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 7:33 PM, Sundar Jubilant wrote: Dear Abraham, I am ignoring hydrogens for the protein residues since I am not sure if the Gromacs has an option to ignore hydrogen only for pretein residues but not for the heme complexed with it. No, there is no ability to ignore them selectively - but if you want to ignore any of them, you have to address the heme hydrogen database issue, or go and remove the hydrogen atoms that you wish to ignore from your input coordinate file. One of my colleagues suggested to treat the Heme as an ligand not as a part of the protein to solve this issue. How would that really affect the accuracy of the simulation? It's not a question of accuracy, but rather that if you have bonded interactions between heme and protein, they have to be part of the same [moleculetype], which is what pdb2gmx is struggling to generate. Mark Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 3:57 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 4:38 PM, Sundar Jubilant wrote: Dear Abraham, Thanks for your email. I have already read the manual to solve the problem but I wasn't successful. That's good to say (particularly the first time you post a request for help, else you'll just get told to go and read), but is unlikely to get much help because you haven't identified aspecific problem. You'd like the ability tobuild hydrogen atoms on a heme residue. pdb2gmxhas to have a specific recipe for doing that.
Re: [gmx-users] Heme group with CHARMM27 FF
On 23/04/2012 12:01 PM, Sundar Jubilant wrote: Dear Abraham, Sorry for making it hard. Since I am so new to this I guess I am not explaining it clearly for you to help me. First of all I dont want to ignore any hydrogens but as pdb2gmx was complaining about my system and suggested me to add -ignh I did so. Since that step introduces other problems, maybe the suggestion wasn't the best approach. Identifying the real problem may lead to a better solution than trouble-shooting an issue that arose from a suggested solution. There's a lesson here about describing the whole problem when seeking help, rather than just the immediate aspect. People who might help want all the information you can give them. My problem is how to update .hdb with heme hydrogen details. So, here to follow your suggestion removing the hydrogen atoms I wish to ignore I actually need to ignore the hydorgens in protein. Maybe. Depends on the original problem. Chopping out just a subset of hydrogens with a text editor, leaving heme alone, solves a class of problems simply without needing to use the brute-force -ign and rebuild approach. Mark Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 8:08 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 9:02 PM, Sundar Jubilant wrote: Dear Abraham, How would it work if I remove the hydrogen atoms that I wish to ignore from my input co-ordinate file? The pdb2gmx tries to add the missing hydorgen atoms for which the .hdb doesn't have information. You've never actually told us what hydrogens you want to ignore, so you're making it hard to help you. Mark In my case here, I can consider heme as a ligand instead of having it as protein since it doesn't need to be the part of the protein. Thanks for your information. Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 6:42 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 7:33 PM, Sundar Jubilant wrote: Dear Abraham, I am ignoring hydrogens for the protein residues since I am not sure if the Gromacs has an option to ignore hydrogen only for pretein residues but not for the heme complexed with it. No, there is no ability to ignore them selectively - but if you want to ignore any of them, you have to address the heme hydrogen database issue, or go and remove the hydrogen atoms that you wish to ignore from your input coordinate file. One of my colleagues suggested to treat the Heme as an ligand not as a part of the protein to solve this issue. How would that really affect the accuracy of the simulation? It's not a question of accuracy, but rather that if you have bonded interactions between heme and protein, they have to be part of the same [moleculetype], which is what pdb2gmx is struggling to generate. Mark Thanks Sundar -Original Message- From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, Apr 20, 2012 3:57 pm Subject: Re: [gmx-users] Heme group with CHARMM27 FF On 20/04/2012 4:38 PM, Sundar Jubilant wrote: Dear Abraham, Thanks for your email. I have already read the manual to solve the problem but I wasn't successful. That's good to say (particularly the first time you post a request for help, else you'll just get told to go and read), but is unlikely to get much help because you haven't identified a specific problem. You'd like the ability to build hydrogen atoms on a heme residue. pdb2gmx has to have a specific recipe for doing that. The manual describes the required format and gives an example. Someone's going to have to do some work. I need little more detailed answer to solve the problem. By the way, here is the full command line for which I got the error. $ pdb2gmx -f CYP.pdb -o CYP_CHARMM.pdb -p CYP1_CHARMM.top -i CYP_CHARMM.itp -ignh If you don't ignore hydrogens, and they're already correct, you don't need to re-generate them... Mark The error is WARNING: atom HA is missing in residue HEM 513 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 513 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HC is missing in residue HEM 513 in the pdb file You might need to add atom HC to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) . . . . . --- Program pdb2gmx, VERSION 4.5.3 Source code file: pdb2top.c, line: 1449 Fatal error: There
[gmx-users] grompp error
Hello, I am doing solvation dynamics for my system. When I am running grompp command I get the error. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o md-rerun.tpr Fatal error: No such combination rule 0 I using Gromacs VERSION 4.0.5. What this error means? Thanks NIlesh -- 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] grompp error
On 4/22/12 11:49 PM, Nilesh Dhumal wrote: Hello, I am doing solvation dynamics for my system. When I am running grompp command I get the error. grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p solvent-bmi-pf6-128.top -o md-rerun.tpr Fatal error: No such combination rule 0 I using Gromacs VERSION 4.0.5. What this error means? It means what it says - your force field (presumably a custom one) is using an invalid combination rule. See manual section 5.3.3 for valid options, then check the [defaults] directive for your force field and amend appropriately. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
