[gmx-users] (no subject)

[Justin Lemkul]

On 8/8/17 1:06 PM, Sorour Hasani wrote:
> Im working on simulating a CYP2D6 with its cofactors (heme ) with GROMACS.
> When I run pdb2gmx, using CHARMM27 FF, I had no error.
> After looking in the literature, I found their corresponding
> parameters: I added the following fields in CHARMM file ffbonded.itp
> [
> bondtypes ]
> ;
> i j func b0 kb
> SG
> FE 1 0.232 209200.0
> 
> [
> angletypes ]
> ;
> i j k func th0 cth ub0 cub
> CT2
> SG FE 5 100.6 418.4 0.0 0.0
> SG
> FE NPH 5 90.0 836.8 0.0 0.0
> SG
> FE NPH 5 90.0 836.8 0.0 0.0
> SG
> FE NPH 5 90.0 836.8 0.0 0.0
> SG
> FE NPH 5 90.0 836.8 0.0 0.0
> ;
> ###
> X
> CS SS X 9 0.20 0.0 3
> CA
> CB SG FE 9 0.20 0.0 3
> HB1
> CB SG FE 9 0.20 0.0 3
> HB1
> CB SG FE 9 0.20 0.0 3
> ;
> ###
> X
> FE SS X 9 0.00 0.0 4
> CB
> SG FE NPH 9 0.00 0.0 4
> CB
> SG FE NPH 9 0.00 0.0 4
> CB
> SG FE NPH 9 0.00 0.0 4
> But after that, I had another type of error:
> Fatal error:
> Unknown bond_atomtype SG, I correct it by default.
> after that in grompp step : I got error
> ERROR 7 [file topol.top, line 41571]:
>> No default Proper Dih. types
>>
>> Fatal error:
>> There were 24 errors in input file(s).
> what should I do?
>>

SG is the atom *name* in cysteine, not its type.  Only atom *types* are valid in 
ffbonded.itp and ffnonbonded.itp.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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