[gmx-users] grompp: "invalid bond type" error
Olivia Waring
owaring at princeton.edu
Wed Nov 2 21:48:30 CET 2011
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?
Sorry to be such a nuisance!
Olivia
On Wed, Nov 2, 2011 at 4:27 PM, Justin A. Lemkul <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 <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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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