[gmx-users] grompp: "invalid bond type" error
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 2 21:51:08 CET 2011
Olivia Waring wrote:
> Yes, it's the same error.
>
> About the bond types: should they be defined as opls_* in ffbonded.itp,
> aminoacids.rtp, both, or somewhere else entirely?
>
The bonds are named in the aminoacids.rtp file, they are defined in
ffbonded.itp. Use names in the .rtp, types in ffbonded.itp. Use existing
residues as a guide.
-Justin
> Sorry to be such a nuisance!
>
> Olivia
>
> On Wed, Nov 2, 2011 at 4:27 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Olivia Waring wrote:
>
> 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!
>
>
>
> Bond types are not defined by atom name, but rather atom type. If
> you're using OPLS, then all the types should be opls_* to be valid.
> I suspect this is at least one source of problem.
>
>
> 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.)
>
>
> Does this topology produce the exact same errors as in your last post?
>
> -Justin
>
> ; 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.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.__au
> <mailto:Mark.Abraham at 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
> <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
>
>
>
>
>
> --
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>
>
> --
> Olivia Waring (王维娅)
> Princeton University '12
> AB Chemistry
>
>
> --
> ==============================__==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> <tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
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--
========================================
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
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