RE: [gmx-users] amber DNA non-integer charge
Yes, you were right, upgrading it to 4.5.4 made sure the atom types/charges in the DNA termini were recognized correctly. This time the topology got generated with integer charges. thanks From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, August 29, 2011 3:06 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] amber DNA non-integer charge Kamesh Narasimhan wrote: I am using Gromacs 4.0.5 and in my ffamber03.rtp I can see that the charges are as you mentioned. H1amber99_170.3520019 But in my top file the H1 atom of the type amber99_17 gets replaced by the amber99_25 type so what should have been amber99_17 1DG5 H1 19 0.352001.008 ; is written by pdb2gmx as amber99_25 1DG5 H1 19 0.4422 1.008 ; How can I make amber generate the topology with the right atomtype and charge in this case?. Thanks in advance. I don't know, but it's not productive to troubleshoot buggy behavior in a Gromacs version that is over two years old. I'd suggest upgrading to the newest version (4.5.4, with the appropriate version of the Amber ports) and seeing if the behavior persists. Otherwise, edit the topology manually to correct the error. -Justin my top file: 1 amber99_43 1DG5O5' 1-0.6318 16 ; qtot -0.6318 2 amber99_25 1DG5H5T 2 0.4422 1.008 ; qtot -0.1896 3 amber99_11 1DG5C5' 3-0.0069 12.01 ; qtot -0.1965 4 amber99_19 1DG5 H5'1 4 0.0754 1.008 ; qtot -0.1211 5 amber99_19 1DG5 H5'2 5 0.0754 1.008 ; qtot -0.0457 6 amber99_11 1DG5C4' 6 0.1629 12.01 ; qtot 0.1172 7 amber99_19 1DG5H4' 7 0.1176 1.008 ; qtot 0.2348 8 amber99_44 1DG5O4' 8-0.3691 16 ; qtot -0.1343 9 amber99_11 1DG5C1' 9 0.0358 12.01 ; qtot -0.0985 10 amber99_20 1DG5H1' 10 0.1746 1.008 ; qtot 0.0761 11 amber99_40 1DG5 N9 11 0.0577 14.01 ; qtot 0.1338 12 amber99_6 1DG5 C8 12 0.0736 12.01 ; qtot 0.2074 13 amber99_24 1DG5 H8 13 0.1997 1.008 ; qtot 0.4071 14 amber99_36 1DG5 N7 14-0.5725 14.01 ; qtot -0.1654 15 amber99_4 1DG5 C5 15 0.1991 12.01 ; qtot 0.0337 16 amber99_2 1DG5 C6 16 0.4918 12.01 ; qtot 0.5255 17 amber99_41 1DG5 O6 17-0.5699 16 ; qtot -0.0444 18 amber99_35 1DG5 N1 18-0.5053 14.01 ; qtot -0.5497 19 amber99_25 1DG5 H1 19 0.4422 1.008 ; qtot -0.1075 20 amber99_3 1DG5 C2 20 0.7432 12.01 ; qtot 0.6357 21 amber99_38 1DG5 N2 21 -0.923 14.01 ; qtot -0.2873 22 amber99_17 1DG5H21 22 0.4235 1.008 ; qtot 0.1362 23 amber99_17 1DG5H22 23 0.4235 1.008 ; qtot 0.5597 24 amber99_37 1DG5 N3 24-0.6636 14.01 ; qtot -0.1039 25 amber99_4 1DG5 C4 25 0.1814 12.01 ; qtot 0.0775 26 amber99_11 1DG5C3' 26 0.0713 12.01 ; qtot 0.1488 27 amber99_19 1DG5H3' 27 0.0985 1.008 ; qtot 0.2473 28 amber99_11 1DG5C2' 28-0.0854 12.01 ; qtot 0.1619 29 amber99_18 1DG5 H2'1 29 0.0718 1.008 ; qtot 0.2337 30 amber99_18 1DG5 H2'2 30 0.0718 1.008 ; qtot 0.3055 31 amber99_44 1DG5O3' 31-0.5232 16 ; qtot -0.2177 . ... . From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, August 29, 2011 2:41 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] amber DNA non-integer charge Kamesh Narasimhan wrote: Hil, I am trying to simulate a protein-DNA structure using amber03 and end up having a non-integer charge in topology generation . From the webpage of ffamber on NA-simulations, I could see this below instruction However, for nucleic acids this also often causes pdb2gmx to replace an H atom in the first residue of all nucleic acid chains with an incorrect H atom, resulting in non-neutral charge. The correct atom is generally replaced with an atom of type amberXX_25 (hydroxyl H), as pdb2gmx treats it as a terminal hydrogen. I replaced
Re: [gmx-users] OPLS-AA Unknown Atomtype
Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? Thanks, Yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, August 23, 2011 2:07 PM Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your reply. Here is the exact error message, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp --- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 620 Fatal error: Unknown bond_atomtype CA1 --- ~~ I understand that I have not inserted CA1 into atomtypes.atp. because if I add CA1 as a new atom, I have to mention all bonds, angles, dihedrals of it. The atomtypes.atp file is irrelevant here; it is only used by pdb2gmx. What you are trying to avoid is what you have to do - if you introduce a new atom type and intend to use it in any bonded interactions, you must introduce relevant parameters for all the interactions in which it will participate. So I denoted the type of it as a known carbon atom in my topology file (in the attachment). I thought in OPLS-AA, CA1 can cite this known atom since CA1 is just a name. Names and types are different. You can name an atom anything you like, but atom types must be judiciously assigned. Meanwhile, in the ffbonded.itp and ffnonbonded.itp, I still use CA1 to give bonds, angles, and dihedrals of CA1. If you have inserted all of the correct parameters in these files, you would not receive the error above. Perhaps herein lies the problem - if you have modified ffnonbonded.itp (which belongs to the force field organization of the 4.5.x series), it will have no effect on a 4.0.7 executable, which is being called above. So (at least) one of two possibilities is true: 1. You're not using the Gromacs version you intend to. 2. You haven't introduced all of the parameters you need to. The bond_atomtype values are assigned in ffnonbonded.itp (counterintuitive, I know, but that's how
[gmx-users] Phd positions available
Dear all, since many people in our group are gromacs users, this announcement could make some sense on the gmx mailing list. Please forward it to interested people. Best wishes, Giovanni Bussi ***PhD positions at SISSA in Physics and Chemistry of Biological Systems There are 3 positions available for the PhD in Physics and Chemistry of Biological Systems at the International School for Advanced Studies, Trieste, Italy. Applicants should have a good background in Physics, Chemistry or related subjects and are expected to obtain their Laurea Specialistica or equivalent degree by Autumn 2011. Applicants will be first screened based on their CV (educational track record, letters of presentation, preprints or publications). Those that pass the preliminary screening will be invited to participate to the local selection taking place on October 5 and 6. Admitted students will have the opportunity to follow a one-year educational program in an international and interdisciplinary environment, followed by two or three years of active research in one of the following areas: * structural bioinformatics, * statistical mechanics of complex molecular systems, * biomolecular simulations, * simulations of rare events. For further information about the available research lines, and past entrance exams see the Statistical and Biological Physics Sector website. To apply: The application should be filled exclusively online at the following address: www.sissa.it/applications/phd . The application deadline is September 19th. The complete official announcement can be download here. Notice that SISSA can cover, in full or in part, the expenses of students who are admitted to the local entrance exam. Please contact p...@sissa.it for further information. About SISSA: The International School for Advanced Studies of Trieste. SISSA was the first Italian university to offer the PhD degree, and has continued to do so with notable success. Since its founding in 1978, SISSA has prepared more than 500 young people for careers in research and teaching. According to a recent independent comprehensive academic survey SISSA is one of the leading Italian research institutes in terms of density of top scientists. In the latest evaluation of the Italian university system (CIVR) it was judged as the most exciting of the small research centers in Italy in physics and mathematics and came second in biology. Facilities: People who study at SISSA, which is situated in the campus in Via Bonomea in a park of over 100,000 m2, have access to an excellent library which is open 24 hours a day; they have a computer at their disposal with which to connect to the huge resources for scientific computing and internet services; they receive support in finding accommodation in the city from the housing service and a monthly contribution from the School towards the rent; on the campus they can find a restaurant, kindergarten, and meditation and music rooms. Students from non-European Union countries have their enrollment in the Italian national health service reimbursed. Female students receive a contribution during their maternity leave. Students are awarded scholarships for the entire duration of their training programmes. ***Start Date November 2011 ***Duration 3 to 4 years ***Funding Source Italian Ministry of University ***Salary on grant Ministerial PhD fellowship integrated by SISSA for a monthly amount of ~ 100 Euros. In addition there are SISSA contributions towards house rent and purchase of personal laptop. ***Contact person Cristian Micheletti ***email miche...@sissa.it ***Group web page: www.sissa.it/sbp -- 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] OPLS-AA Unknown Atomtype
Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 This total charge suggests that your topology is badly broken. processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again. -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] Error found on grompp - energy minimization
Dear sir, I struck with the following error when i perform energy minimization. I unable to understand what did it mean? please make me clear. So kindly do the needful. Fatal error: Atomtype CR1 not found -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- 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] Error found on grompp - energy minimization
On 29/08/2011 9:18 PM, ITHAYARAJA wrote: Dear sir, I struck with the following error when i perform energy minimization. I unable to understand what did it mean? please make me clear. So kindly do the needful. Fatal error: Atomtype CR1 not found One of your molecules is trying to use an atomtype that isn't defined in your force field. However we can't guess why without a lot more information. See http://www.gromacs.org/Support 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
[gmx-users] Re: gromacs question topologie
Please keep all Gromacs-related correspondence on the gmx-users list, particularly if the discussion was previously carried out there. I am not a private tutor. Joschua Sterzenbach wrote: Hi is in the coordinate file only the geometry of the molecule? Yes. Have a look at its contents - all you'll find in most common formats are the (x,y,z) coordinates of the named atoms. I ask because I only have the geometry. Do I get the topologie out of the geometry or from where comes it? Please do some basic tutorial material to understand the Gromacs workflow. For residue-based biomolecules like proteins and nucleic acids, use pdb2gmx. For other molecules, g_x2top can create basic topologies for a limited number of force fields and molecules. Otherwise, you'll have to obtain the topology by some other means. There are other programs on the User Contributions page of the Gromacs site that can produce topologies for arbitrary molecules. You haven't said yet what you're working with, so all I can do is venture guesses. -Justin The questions corresponds to this: http://www.mail-archive.com/gmx-users@gromacs.org/msg43478.html Thanks Regards -- 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] Re: Difficulty building a topology for a synthetic, branched PEG-peptide molecule [SOLVED]
That's a long bond. Does your reference length in specbond.dat suit it? IIRC there should be some evidence in the output of the special bond being formed if it actually is. If not, your symptoms are probably related Hi Mark, indeed, I think that was part of the problem. pdb2gmx indeed outputs a message when a specbond.dat rule is matched and a bond formed. In case it helps to someone else or for reference purposes, I finally managed to solve the issue. Some of the lessons I learned: - make sure that the residues/atoms in specbond.dat were correct (I had defined a number of residues for termini and mid-chain PEG and connectors, and I got them confused at some point, so not all of them were being recognized properly). The dangling bond at at least one of the terminal ends given by pdb2gmx is most likely due to this and/or the protonation state of the residues connecting the fragments - each fragment is assigned a different chain letter in the source PDB file; in my case, for a system like [N-(peptide1)-C]-[N-(PEG)-C]-[N-(peptide2)-Lys-C] | NZ | [C-(PEG)-N]-[C-(peptide3)-N] each fragment in square brackets is assigned a different chain name in [A-E] in the PDB file: ATOM123 N ARG A 1 74.024 13.299 50.237 1.00 0.00 N1+ ^ - always list the atoms within a chain in an N-to-C direction. This means that the main branch is defined first, and then the branching point is defined in an N-to-C direction, even if it is counterintuitive by the way they are connected. specbond.dat takes good care of setting up the connection in all cases (as long as they are well defined...). - the PEG residues need to be defined as type Other in residues.dat - call pdb2gmx to manually assign the termini and Lys protonation states manually, and to merge the chains into a single molecule: pdb2gmx-ter -f substrate.pdb-chainsep interactive-lys - the internal termini (i.e., the ones that are peptide termini but are connected to a PEG chain) need to be given a protonation state of None, while the real termini can be assigned as charged or neutral, depending on the conditions Oh, and well done for constructing a good question. You would likely not have gotten anywhere giving less detail :) Thanks, it actually helped putting everything in writing, as it pointed out the few things that I hadn't yet looked at in detail... Pablo Englebienne, PhD Dept. of Biomedical Engineering Dept. of Chemistry and Chemical Engineering Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 -- 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] simulation at higher temperatures
Hi friends, As a part of my work i have to do simulation at higher temperature (400K or more) to study the folding, unfolding and stability of protein, for that i kept simulation for 3ns at 400k (400k temperature both in equilibration and production) keeping all the other parameters as usual (time step 2fs, explicit solvent model SPC, equilibration with NVT and NPT ensembles for 100ps each ). the simulation was completed but , 1. in trajectory i found that protein is comming out of the box (cubic box -d 1.0) i think may be the box size was not sufficient (and i know that when we increase the temperature the velocity of atoms will increase). 2. when i save the structure with minimum energy and saw in pymol i found the side chains, hydrogens was broken through out the protein. 3. later i used the command ( trajconv -s md.tpr -f md.trr -o protein.pdb -pbc nojump -dt 10 ) to save the conformations at each 10 ps and to see the conformational changes by playing it as a movie in pymol , but i found a single conformation was just shaking through out the movie (this is happening in normal simulation also) later i read in gmx user problems that most of the force field parameters are calculated at room temperature, so in that case what are the parameters and forcefield that we need to fallow for higher temperature simulations. so can any one please takes time to explain this, it would be helpful for me to study further. Thanking you. with regards -- Arun Kumar Somavarapu Center for Bioinformatics Pondicherry University Kalapet Puducherry-605014 -- 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] simulation at higher temperatures
arun kumar wrote: Hi friends, As a part of my work i have to do simulation at higher temperature (400K or more) to study the folding, unfolding and stability of protein, for that i kept simulation for 3ns at 400k (400k temperature both in equilibration and production) keeping all the other parameters as usual (time step 2fs, explicit solvent model SPC, equilibration with NVT and NPT ensembles for 100ps each ). the simulation was completed but , I doubt any simulation, even of the simplest protein, is complete at 3 ns. 1. in trajectory i found that protein is comming out of the box (cubic box -d 1.0) i think may be the box size was not sufficient (and i know that when we increase the temperature the velocity of atoms will increase). Please see FAQ #3 under the following section: http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization 2. when i save the structure with minimum energy and saw in pymol i found the side chains, hydrogens was broken through out the protein. Same as above. 3. later i used the command ( trajconv -s md.tpr -f md.trr -o protein.pdb -pbc nojump -dt 10 ) to save the conformations at each 10 ps and to see the conformational changes by playing it as a movie in pymol , but i found a single conformation was just shaking through out the movie (this is happening in normal simulation also) Your simulation length is inadequate to view any conformational changes. These types of motions can require hundreds of ns, if not more (depending on the size of the protein), to visualize. -Justin later i read in gmx user problems that most of the force field parameters are calculated at room temperature, so in that case what are the parameters and forcefield that we need to fallow for higher temperature simulations. so can any one please takes time to explain this, it would be helpful for me to study further. Thanking you. with regards -- Arun Kumar Somavarapu Center for Bioinformatics Pondicherry University Kalapet Puducherry-605014 -- 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_lie
g_lie calculates the deltaG= alpha(Vl-s LJp - Vl-s LJw) + beta(Vl-s elp - Vl-s elw) equation. But when calculating DGbind from g_lie it will ask for only one term at a time i.e. -Elj for either Vl-s LJp or Vl-s LJw and -Cqq for either Vl-s elp or Vl-s elw. My question is when using only Vl-s LJp for -Elj and Vl-s elp for -Cqq, how the LJ and EL terms calculated for ligand-water interaction or in vice-versa condition for ligand-protein interactions to complete the deltaG equation? -- Pawan -- 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] OPLS-AA Unknown Atomtype
HI Justin, I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions. So I do not think ions addition will help. And I double-checked the angles, bonds, mentioned in the ffoplsaabon.itp, they are there. So I do not know any other files I may need to modify. Thanks, yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, August 29, 2011 3:41 AM Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 This total charge suggests that your topology is badly broken. processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again. -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] OPLS-AA Unknown Atomtype
Yao Yao wrote: HI Justin, I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions. So I do not think ions addition will help. And I double-checked the The net charge problem cannot be solved by adding ions. A fractional charge of that magnitude indicates the charges in the topology are wrong. angles, bonds, mentioned in the ffoplsaabon.itp, they are there. So I do not know any other files I may need to modify. The only file that contains [bondtypes], [angletypes], etc is ffoplsaabon.itp, so if the entries are indeed there, have the correct format, and are placed appropriately, you wouldn't be getting this error. So unless you post the exact lines in their exact context, I'm left to assume that you've done something else wrong. -Justin Thanks, yao *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, August 29, 2011 3:41 AM *Subject:* Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 This total charge suggests that your topology is badly broken. processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again. -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 mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] MARTINI / all-atom mapping
Hi all, I am trying to reverse-map some martini lipids to united atom. In order to do this, I'd prefer to have an EXACT definition of the aa-to-cg mapping. I cannot find this, only an imprecise graphic, in the MARTINI paper; the martini.itp file doesn't appear to list which heavy atoms are represented by each CG bead either. For example, I'm looking for something like: 'NC3' : ['C1', 'C2', 'C3', 'N4', 'C5', 'C6'], 'PO4' : ['O7', 'P8', 'O9', 'O10', 'O11','C12'], 'GL1' : ['C13', 'O14', 'C15', 'O16'], 'GL2' : ['C32', 'O33', 'C34', 'O35'], etc. For some atoms it's obvious which MARTINI groups they belong in, but others on the borderline are not obvious. For example, does C12 belong in PO4 or GL1? Anybody have a master list like this? Thanks, Mike -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- 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] restarting a crashed job
Hello, My simulation crashed in the middle and I used the -cpi checkpoint.cpt -append option to continue. However, GROMACS cannot continue and complains about not being able to open the corresponding .trr file. I checked my folder, the trr file is there and the name is the same as the *.tpr and *.cpt files. What else could have caused this problem? Thanks. P. -- 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] restarting a crashed job
On 30/08/2011 1:14 PM, Payman Pirzadeh wrote: Hello, My simulation crashed in the middle and I used the /--cpi checkpoint.cpt --append/ option to continue. However, GROMACS cannot continue and complains about not being able to open the corresponding .trr file. I checked my folder, the trr file is there and the name is the same as the *.tpr and *.cpt files. What else could have caused this problem? Some kind of filesystem-based locking mechanism sounds most likely. If a zombie process of the old run still has the file, you might not be able to open it again. Also, check the file permissions. 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
