Hi Justin and Mark, Thank you so much for your replies. Mark, would you mind clarifying what you mean? What exactly should I be looking for in the ffbonded.itp file? I'm not sure why those bonded parameters in particular were overridden... I didn't intend to modify anything!
Perhaps it would help if I gave a more complete description of my system. I'm using the oplsaa force field to model a simple alkanethiol chain. I've defined a new residue as follows: [ ALK ] [ atoms ] CA opls_139 -0.180 1 HAA opls_140 0.060 1 HAB opls_140 0.060 1 HAC opls_140 0.060 1 CB opls_139 -0.120 2 HBA opls_140 0.060 2 HBB opls_140 0.060 2 CC opls_139 -0.120 3 HCA opls_140 0.060 3 HCB opls_140 0.060 3 CD opls_139 -0.120 4 HDA opls_140 0.060 4 HDB opls_140 0.060 4 CE opls_139 -0.120 5 HEA opls_140 0.060 5 HEB opls_140 0.060 5 CF opls_139 -0.120 6 HFA opls_140 0.060 6 HFB opls_140 0.060 6 CG opls_139 -0.120 7 HGA opls_140 0.060 7 HGB opls_140 0.060 7 CH opls_139 -0.120 8 HHA opls_140 0.060 8 HHB opls_140 0.060 8 CI opls_139 -0.120 9 HIA opls_140 0.060 9 HIB opls_140 0.060 9 CJ opls_139 -0.120 10 HJA opls_140 0.060 10 HJB opls_140 0.060 10 CK opls_139 -0.120 11 HKA opls_140 0.060 11 HKB opls_140 0.060 11 CL opls_206 -0.120 12 HLA opls_140 0.060 12 HLB opls_140 0.060 12 SA opls_200 -0.335 13 HS opls_204 0.155 13 [ bonds ] CA HAA CA HAB CA HAC CA CB CB HBA CB HBB CB CC CC HCA CC HCB CC CD CD HDA CD HDB CD CE CE HEA CE HEB CE CF CF HFA CF HFB CF CG CG HGA CG HGB CG CH CH HHA CH HHB CH CI CI HIA CI HIB CI CJ CJ HJA CJ HJB CJ CK CK HKA CK HKB CK CL CL HLA CL HLB CL SA SA HS In ffbonded.itp, I've defined the following bondtypes: ; begin Olivia-defined bondtypes CA HAA 1 0.10800 284512.0 ; spring constant came from OPLS C* HC bondtype CA HAB 1 0.10800 284512.0 CA HAC 1 0.10800 284512.0 CA CB 1 0.15300 265265.6 ; spring constant came from OPLS C C3 bondtype CB HBA 1 0.10800 284512.0 CB HBB 1 0.10800 284512.0 CB CC 1 0.15300 265265.6 CC HCA 1 0.10800 284512.0 CC HCB 1 0.10800 284512.0 CC CD 1 0.15300 265265.6 CD HDA 1 0.10800 284512.0 CD HDB 1 0.10800 284512.0 CD CE 1 0.15300 265265.6 CE HEA 1 0.10800 284512.0 CE HEB 1 0.10800 284512.0 CE CF 1 0.15300 265265.6 CF HFA 1 0.10800 284512.0 CF HFB 1 0.10800 284512.0 CF CG 1 0.15300 265265.6 CG HGA 1 0.10800 284512.0 CG HGB 1 0.10800 284512.0 CG CH 1 0.15300 265265.6 CH HHA 1 0.10800 284512.0 CH HHB 1 0.10800 284512.0 CH CI 1 0.15300 265265.6 CI HIA 1 0.10800 284512.0 CI HIB 1 0.10800 284512.0 CI CJ 1 0.15300 265265.6 CJ HJA 1 0.10800 284512.0 CJ HJB 1 0.10800 284512.0 CJ CK 1 0.15300 265265.6 CK HKA 1 0.10800 284512.0 CK HKB 1 0.10800 284512.0 CK CL 1 0.15300 265265.6 CL HLA 1 0.10800 284512.0 CL HLB 1 0.10800 284512.0 CL SA 1 0.18200 284512.0 ; not sure what the spring constant should be here... will peruse literature! Here is my topology file (different from the last one I posted, since that was for a customized forcefield I had designed from scratch... I have since abandoned that pursuit, and here I am using the predefined opls parameters.) ; Include forcefield parameters #include "oplsaa.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 ALK rtp ALK q -0.2 1 opls_139 1 ALK CA 1 -0.18 12.011 ; qtot -0.18 2 opls_140 1 ALK HAA 1 0.06 1.008 ; qtot -0.12 3 opls_140 1 ALK HAB 1 0.06 1.008 ; qtot -0.06 4 opls_140 1 ALK HAC 1 0.06 1.008 ; qtot 0 5 opls_139 1 ALK CB 2 -0.12 12.011 ; qtot -0.12 6 opls_140 1 ALK HBA 2 0.06 1.008 ; qtot -0.06 7 opls_140 1 ALK HBB 2 0.06 1.008 ; qtot 0 8 opls_139 1 ALK CC 3 -0.12 12.011 ; qtot -0.12 9 opls_140 1 ALK HCA 3 0.06 1.008 ; qtot -0.06 10 opls_140 1 ALK HCB 3 0.06 1.008 ; qtot 0 11 opls_139 1 ALK CD 4 -0.12 12.011 ; qtot -0.12 12 opls_140 1 ALK HDA 4 0.06 1.008 ; qtot -0.06 13 opls_140 1 ALK HDB 4 0.06 1.008 ; qtot 0 14 opls_139 1 ALK CE 5 -0.12 12.011 ; qtot -0.12 15 opls_140 1 ALK HEA 5 0.06 1.008 ; qtot -0.06 16 opls_140 1 ALK HEB 5 0.06 1.008 ; qtot 0 17 opls_139 1 ALK CF 6 -0.12 12.011 ; qtot -0.12 18 opls_140 1 ALK HFA 6 0.06 1.008 ; qtot -0.06 19 opls_140 1 ALK HFB 6 0.06 1.008 ; qtot 0 20 opls_139 1 ALK CG 7 -0.12 12.011 ; qtot -0.12 21 opls_140 1 ALK HGA 7 0.06 1.008 ; qtot -0.06 22 opls_140 1 ALK HGB 7 0.06 1.008 ; qtot 0 23 opls_139 1 ALK CH 8 -0.12 12.011 ; qtot -0.12 24 opls_140 1 ALK HHA 8 0.06 1.008 ; qtot -0.06 25 opls_140 1 ALK HHB 8 0.06 1.008 ; qtot 0 26 opls_139 1 ALK CI 9 -0.12 12.011 ; qtot -0.12 27 opls_140 1 ALK HIA 9 0.06 1.008 ; qtot -0.06 28 opls_140 1 ALK HIB 9 0.06 1.008 ; qtot 0 29 opls_139 1 ALK CJ 10 -0.12 12.011 ; qtot -0.12 30 opls_140 1 ALK HJA 10 0.06 1.008 ; qtot -0.06 31 opls_140 1 ALK HJB 10 0.06 1.008 ; qtot 0 32 opls_139 1 ALK CK 11 -0.12 12.011 ; qtot -0.12 33 opls_140 1 ALK HKA 11 0.06 1.008 ; qtot -0.06 34 opls_140 1 ALK HKB 11 0.06 1.008 ; qtot 0 35 opls_206 1 ALK CL 12 -0.12 12.011 ; qtot -0.12 36 opls_140 1 ALK HLA 12 0.06 1.008 ; qtot -0.06 37 opls_140 1 ALK HLB 12 0.06 1.008 ; qtot 0 38 opls_200 1 ALK SA 13 -0.335 32.06 ; qtot -0.335 39 opls_204 1 ALK HS 13 0.155 1.008 ; qtot -0.18 [ bonds ] ; ai aj funct c0 c1 c2 c3 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 fcx fcy fcz 1 1 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.au>wrote: > 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 1 0.13270 179075.2 > > > WARNING 2 [file ffbonded.itp, line 64]: > Overriding Bond parameters. > > old: 0.1522 265266 0.1522 265266 > new: C CT 1 0.14950 265265.6 > > > WARNING 3 [file ffbonded.itp, line 67]: > Overriding Bond parameters. > > old: 0.149 334720 0.149 334720 > new: CA C 1 0.14240 392459.2 > > > WARNING 4 [file ffbonded.itp, line 73]: > Overriding Bond parameters. > > old: 0.1419 374050 0.1419 374050 > new: C CB 1 0.14240 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 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 > -- Olivia Waring (王维娅) Princeton University '12 AB Chemistry
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