[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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