[gmx-users] grompp: "invalid bond type" error
Olivia Waring
owaring at princeton.edu
Wed Nov 2 17:29:01 CET 2011
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.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
>
>
> 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
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