[gmx-users] Software inconsistency error: One or more interactions were multiple assigned in the domain decomposition
the source of the error - the documentation on this sort of thing is sparse. Thanks so much in advance, -- Olivia Waring Princeton University '12 AB Chemistry -- 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] Domain decomposition problems
Dear Gromacs users, Could someone please shed light on the following problem? My system consists of an alkanethiol SAM (in the xy plane) with a layer of water on top. The mdrun command works when the box vectors are 1.1, 1.3, and 2.5, but the SAM flies apart and the simulation crashes. I'm trying to lengthen the box in the z direction (and of course, resolvating the system) to see if that solves the problem. Unfortunately, this seems to give rise to domain decomposition issues... I get the following output in my md.log file: Initial maximum inter charge-group distances: two-body bonded interactions: 0.424 nm, LJ-14, atoms 36 39 multi-body bonded interactions: 0.424 nm, Ryckaert-Bell., atoms 36 39 Minimum cell size due to bonded interactions: 0.467 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.794 nm Estimated maximum distance required for P-LINCS: 0.794 nm This distance will limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 6 cells with a minimum initial size of 0.992 nm The maximum allowed number of cells is: X 1 Y 1 Z 5 Fatal error: There is no domain decomposition for 6 nodes that is compatible with the given box and a minimum cell size of 0.9925 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings I've experimented a bit with -rcon and with the number of nodes, but I really have no idea what I'm doing! Any thoughts would be appreciated. Olivia -- 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] Re: Generating Pairs with a Buckingham Potential
Hi Mark, Thanks for your reply! I'm sorry, you're right, as far as I know the manual doesn't actually mention Buckingham pairs generation... but when I set gen-pairs to yes and run grompp, I get the following error: Generating pair parameters is only supported with LJ non-bonded interactions I guess I'm wondering how anyone can use the Buckingham potential at all, since Gromacs does not appear to support pairs generation for the Buckingham or the use of explicitly defined Buckingham pair parameters (when defining [ pairtypes ], you have to give the parameters in LJ form). Thanks so much again, Olivia On Wed, Dec 28, 2011 at 8:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/12/11, *Olivia Waring *owar...@princeton.edu wrote: I apologize for the truncated message; I pressed send too soon. According to the Gromacs manual, pairs cannot be generated automatically for the Buckingham potential, Where does it say this? but the [ pairtypes ] directive seems to only accept parameters in LJ form (i.e. c6 and c12, instead of a, b, and c6). I've been looking into ways to interconvert between the two potential forms, but haven't found anything... Can anyone who has successfully generated a topology using the Buckingham potential shed light on this issue? You want a 1-4 interaction using Buckingham functional form? If so, I don't think GROMACS supports it. If you're trying to combine bits of force fields that use L-J with bits of force fields that use Buckingham, then that's almost certainly a bad idea. Mark Thank you so much, Olivia On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring owar...@princeton.eduwrote: Hello Gromacs users, I'm using a Buckingham potential for the nonbonded interactions in my system, so I have the following lines in my forcefield.itp file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 1.0 1.0 -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- 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 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] (no subject)
Hello Gromacs users, I'm using a Buckingham potential for the nonbonded interactions in my system, so I have the following lines in my forcefield.itp file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 1.0 1.0 -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- 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:
I apologize for the truncated message; I pressed send too soon. According to the Gromacs manual, pairs cannot be generated automatically for the Buckingham potential, but the [ pairtypes ] directive seems to only accept parameters in LJ form (i.e. c6 and c12, instead of a, b, and c6). I've been looking into ways to interconvert between the two potential forms, but haven't found anything... Can anyone who has successfully generated a topology using the Buckingham potential shed light on this issue? Thank you so much, Olivia On Wed, Dec 28, 2011 at 11:05 AM, Olivia Waring owar...@princeton.eduwrote: Hello Gromacs users, I'm using a Buckingham potential for the nonbonded interactions in my system, so I have the following lines in my forcefield.itp file: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 1.0 1.0 -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- 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] Using tables to construct a z-dependent 12-3 potential
Hello all, I'm wondering if it's possible to use tables to simulate a z-dependent 12-3 potential. I'd have the following function: V(z) = C12/(z-z0)^12 - C3/(z-z0)^3 and I'm trying to construct a table to match. Any hints to get me started would be greatly appreciated. Thank you! Olivia -- Olivia Waring Princeton University '12 AB Chemistry -- 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] Using tables to construct a z-dependent 12-3 potential
Thanks David! That helped a lot. I'm now trying to use the walls feature with a user-defined potential. My mdp file is shown below: title = Alkanethiol SAM MD ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps energygrps = CH3 CH2 S wall0 energygrp_table = CH3 wall0 CH2 wall0 S wall0 ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) coulombtype = Cutoff rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) vdwtype = User rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; Pressure coupling on in NPT ; Periodic boundary conditions pbc = xy; 3-D PBC ; Dispersion correction DispCorr= no; account for cut-off vdW scheme ; Walls nwall = 1 wall_type = table wall_atomtype = wall0 ; Velocity generation gen_vel = no; Velocity generation is off I've defined three energy groups in my system (CH3, CH2, and S), and I have built the following three energy group tables: table_CH3_wall0.xvg table_CH2_wall0.xvg table_S_wall0.xvg I'm not sure whether I should list wall0 among the [ atomtypes ]... When I do, grompp complains about wall0 not being found in the index file. I could add it, but since wall0 doesn't correspond to any actual atoms in my system, I'm not exactly sure how to proceed. In summary, I'm confused as to how to combine the concepts of energy groups and walls when using potential tables. Thank you so much! Olivia On Sat, Nov 26, 2011 at 10:13 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2011-11-26 15:58, Olivia Waring wrote: Hello all, I'm wondering if it's possible to use tables to simulate a z-dependent 12-3 potential. I'd have the following function: V(z) = C12/(z-z0)^12 - C3/(z-z0)^3 and I'm trying to construct a table to match. Any hints to get me started would be greatly appreciated. If you mean z as just one cartesian coordinate you should look into the wall potential options. Otherwise you plot the function in tables as a function of z-z0, since it will be used with the distance. This is in the manual... Thank you! Olivia -- Olivia Waring Princeton University '12 AB Chemistry -- 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-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] grompp: invalid bond type error
CB 2 -0.12 12.011 ; qtot -0.12 6 opls_140 1ALKHBA 2 0.06 1.008 ; qtot -0.06 7 opls_140 1ALKHBB 2 0.06 1.008 ; qtot 0 8 opls_139 1ALK CC 3 -0.12 12.011 ; qtot -0.12 9 opls_140 1ALKHCA 3 0.06 1.008 ; qtot -0.06 10 opls_140 1ALKHCB 3 0.06 1.008 ; qtot 0 11 opls_139 1ALK CD 4 -0.12 12.011 ; qtot -0.12 12 opls_140 1ALKHDA 4 0.06 1.008 ; qtot -0.06 13 opls_140 1ALKHDB 4 0.06 1.008 ; qtot 0 14 opls_139 1ALK CE 5 -0.12 12.011 ; qtot -0.12 15 opls_140 1ALKHEA 5 0.06 1.008 ; qtot -0.06 16 opls_140 1ALKHEB 5 0.06 1.008 ; qtot 0 17 opls_139 1ALK CF 6 -0.12 12.011 ; qtot -0.12 18 opls_140 1ALKHFA 6 0.06 1.008 ; qtot -0.06 19 opls_140 1ALKHFB 6 0.06 1.008 ; qtot 0 20 opls_139 1ALK CG 7 -0.12 12.011 ; qtot -0.12 21 opls_140 1ALKHGA 7 0.06 1.008 ; qtot -0.06 22 opls_140 1ALKHGB 7 0.06 1.008 ; qtot 0 23 opls_139 1ALK CH 8 -0.12 12.011 ; qtot -0.12 24 opls_140 1ALKHHA 8 0.06 1.008 ; qtot -0.06 25 opls_140 1ALKHHB 8 0.06 1.008 ; qtot 0 26 opls_139 1ALK CI 9 -0.12 12.011 ; qtot -0.12 27 opls_140 1ALKHIA 9 0.06 1.008 ; qtot -0.06 28 opls_140 1ALKHIB 9 0.06 1.008 ; qtot 0 29 opls_139 1ALK CJ 10 -0.12 12.011 ; qtot -0.12 30 opls_140 1ALKHJA 10 0.06 1.008 ; qtot -0.06 31 opls_140 1ALKHJB 10 0.06 1.008 ; qtot 0 32 opls_139 1ALK CK 11 -0.12 12.011 ; qtot -0.12 33 opls_140 1ALKHKA 11 0.06 1.008 ; qtot -0.06 34 opls_140 1ALKHKB 11 0.06 1.008 ; qtot 0 35 opls_206 1ALK CL 12 -0.12 12.011 ; qtot -0.12 36 opls_140 1ALKHLA 12 0.06 1.008 ; qtot -0.06 37 opls_140 1ALKHLB 12 0.06 1.008 ; qtot 0 38 opls_200 1ALK SA 13 -0.335 32.06 ; qtot -0.335 39 opls_204 1ALK HS 13 0.155 1.008 ; qtot -0.18 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 5 8 1 ... etc. ... ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include oplsaa.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include oplsaa.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein 1 I'm so sorry to inundate you with information, but I hope this might help us get to the root of the problem!! I've been staring at this for days. :) Thanks again, Olivia On Tue, Nov 1, 2011 at 8:48 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 2/11/2011 8:32 AM, Olivia Waring wrote: Dear Gromacs users, First of all, many thanks to Justin for his assistance with my previous question. I have defined a new residue type in the oplsaa force field, changing the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try to preprocess, I get the following output: WARNING 1 [file ffbonded.itp, line 58]: You'll need to inspect at and before this line in this file to diagnose. Mark Overriding Bond parameters. old: 0.1229 476976 0.1229 476976 new: C O 10.13270 179075.2 WARNING 2 [file ffbonded.itp, line 64]: Overriding Bond parameters. old: 0.1522 265266 0.1522 265266 new: CCT 10.14950 265265.6 WARNING 3 [file ffbonded.itp, line 67]: Overriding Bond parameters. old: 0.149 334720 0.149 334720 new: CAC 10.14240 392459.2 WARNING 4 [file ffbonded.itp, line 73]: Overriding Bond parameters. old: 0.1419 374050 0.1419 374050 new: CCB 10.14240 392459.2 --- Program grompp, VERSION 4.5.4 Source code file: topdirs.c, line: 76 Fatal error: Invalid bond type
[gmx-users] grompp: invalid bond type error
Dear Gromacs users, First of all, many thanks to Justin for his assistance with my previous question. I have defined a new residue type in the oplsaa force field, changing the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try to preprocess, I get the following output: WARNING 1 [file ffbonded.itp, line 58]: Overriding Bond parameters. old: 0.1229 476976 0.1229 476976 new: C O 10.13270 179075.2 WARNING 2 [file ffbonded.itp, line 64]: Overriding Bond parameters. old: 0.1522 265266 0.1522 265266 new: CCT 10.14950 265265.6 WARNING 3 [file ffbonded.itp, line 67]: Overriding Bond parameters. old: 0.149 334720 0.149 334720 new: CAC 10.14240 392459.2 WARNING 4 [file ffbonded.itp, line 73]: Overriding Bond parameters. old: 0.1419 374050 0.1419 374050 new: CCB 10.14240 392459.2 --- Program grompp, VERSION 4.5.4 Source code file: topdirs.c, line: 76 Fatal error: Invalid bond type 0 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The error is rather cryptic, and I'm having trouble tracking it down... I even went to the source code (topdirs.c), but I'm still not sure where exactly this invalid bond type is being defined. Thank you so much for your help, Olivia -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- 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: invalid bond type error
Thank you so much for your quick reply! Below please find my topology file: ; Include forcefield parameters #include hautklein.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein_chain_1 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 0 ALK rtp ALK q 0.0 1CH3 0ALKCH3 1 0 15.035 ; qtot 0 2CH2 0ALK CH2A 2 0 14.027 ; qtot 0 3CH2 0ALK CH2B 3 0 14.027 ; qtot 0 4CH2 0ALK CH2C 4 0 14.027 ; qtot 0 5CH2 0ALK CH2D 5 0 14.027 ; qtot 0 6CH2 0ALK CH2E 6 0 14.027 ; qtot 0 7CH2 0ALK CH2F 7 0 14.027 ; qtot 0 8CH2 0ALK CH2G 8 0 14.027 ; qtot 0 9CH2 0ALK CH2H 9 0 14.027 ; qtot 0 10CH2 0ALK CH2I 10 0 14.027 ; qtot 0 11CH2 0ALK CH2J 11 0 14.027 ; qtot 0 12CH2 0ALK CH2K 12 0 14.027 ; qtot 0 13 S 0ALK S 13 0 32.06 ; qtot 0 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 2 3 1 3 4 1 4 5 1 5 6 1 6 7 1 7 8 1 8 9 1 910 1 1011 1 1112 1 1213 1 [ pairs ] ; aiaj functc0c1c2c3 1 4 1 2 5 1 3 6 1 4 7 1 5 8 1 6 9 1 710 1 811 1 912 1 1013 1 [ angles ] ; aiajak functc0c1c2 c3 1 2 3 1 2 3 4 1 3 4 5 1 4 5 6 1 5 6 7 1 6 7 8 1 7 8 9 1 8 910 1 91011 1 101112 1 111213 1 [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 1 2 3 4 3 2 3 4 5 3 3 4 5 6 3 4 5 6 7 3 5 6 7 8 3 6 7 8 9 3 7 8 910 3 8 91011 3 9101112 3 10111213 3 [ constraints ] ; i j funct b0 1 2 1 0.0153 2 3 1 0.0153 3 4 1 0.0153 4 5 1 0.0153 5 6 1 0.0153 6 7 1 0.0153 7 8 1 0.0153 8 9 1 0.0153 9 101 0.0153 10111 0.0153 11121 0.0153 12131 0.0182 ; Include Position restraint file #ifdef POSRES #include posre.itp #endif [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_1 1 Does this help? Thanks so much again, Olivia On Tue, Nov 1, 2011 at 5:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: Olivia Waring wrote: Dear Gromacs users, First of all, many thanks to Justin for his assistance with my previous question. I have defined a new residue type in the oplsaa force field, changing the aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try to preprocess, I get the following output: WARNING 1 [file ffbonded.itp, line 58]: Overriding Bond parameters. old: 0.1229 476976 0.1229 476976 new: C O 10.13270 179075.2 WARNING 2 [file ffbonded.itp, line 64]: Overriding Bond parameters. old: 0.1522 265266 0.1522 265266 new: CCT 10.14950 265265.6 WARNING 3 [file ffbonded.itp, line 67]: Overriding Bond parameters. old: 0.149 334720 0.149 334720 new: CAC 10.14240 392459.2 WARNING 4 [file ffbonded.itp, line 73]: Overriding Bond parameters. old: 0.1419 374050 0.1419 374050 new: CCB 10.14240 392459.2 These four warnings suggest you're using values for bonded parameters that conflict with those present in the force field. If you have reason to do this, then there's no problem, per se. But be aware that you're using parameters the force field does not expect. --**- Program grompp, VERSION 4.5.4 Source code file: topdirs.c, line: 76 Fatal error: Invalid bond type 0 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors The error is rather
[gmx-users] Simulating an alkanethiol SAM on gold: atom type not recognized when running pdb2gmx
Hello GROMACS users, I wish to simulate an alkanethiol self-assembled monolayer on a gold surface. The first molecule I am attempting to model is quite simple: CH3(CH2)11S. I have constructed a united atom force field based on parameters published by Hautman and Klein (J. Chem. Phys. 1989) to represent the alkanethiol chain. I wrote an rtp file containing a single residue [ ALK ] which contains the following list of atoms: [ ALK ] [ atoms ] ; name type charge chargegroup CH3 CH3 0.000 1 CH2A CH2 0.000 1 CH2B CH2 0.000 1 CH2C CH2 0.000 1 CH2D CH2 0.000 1 CH2E CH2 0.000 1 CH2F CH2 0.000 1 CH2G CH2 0.000 1 CH2H CH2 0.000 1 CH2I CH2 0.000 1 CH2J CH2 0.000 1 CH2K CH2 0.000 1 SS0.000 1 I have defined the CH3, CH2, and S atom types in an atomtypes.atp file. I used PRODRG to generate an all-atom pdb file representing my alkanethiol, which I then manually modified to reflect my united atom approach. Here is an excerpt: HETATM1 CH3ALK 1 -0.920 -1.820 -0.970 1.00 20.00 C HETATM2 CH2A ALK 1 -0.010 -2.270 0.170 1.00 20.00 C HETATM3 CH2B ALK 1 0.240 -3.780 0.060 1.00 20.00 C HETATM4 CH2C ALK 1 1.140 -4.290 1.190 1.00 20.00 C HETATM5 CH2D ALK 1 0.420 -4.310 2.540 1.00 20.00 C HETATM6 CH2E ALK 1 1.310 -4.850 3.660 1.00 20.00 C HETATM7 CH2F ALK 1 1.530 -6.360 3.540 1.00 20.00 C HETATM8 CH2G ALK 1 2.420 -6.850 4.680 1.00 20.00 C HETATM9 CH2H ALK 1 2.630 -8.360 4.540 1.00 20.00 C HETATM 10 CH2I ALK 1 3.510 -8.860 5.700 1.00 20.00 C HETATM 11 CH2J ALK 1 3.750 -10.370 5.610 1.00 20.00 C HETATM 12 CH2K ALK 1 2.490 -11.170 5.960 1.00 20.00 C HETATM 12 S ALK 1 2.730 -12.980 5.840 1.00 20.00 S When I try to run pdb2gmx on my coordinate file, I get the following error: Atom CH2 in residue ALK 0 was not found in rtp entry ALK with 13 atoms while sorting atoms. Although I have read through a significant portion of the manual, I am a very new GROMACS user, and have most likely made numerous mistakes!! If someone could please point out how to address this error and anything else I might be missing, I would appreciate it very much. Any general tips for constructing a system from scratch are also quite welcome. Thank you in advance, O. M. W. -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry -- 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
