[gmx-users] Protein ligand simulation

[Justin Lemkul]

On 10/1/19 3:39 AM, DEEPANSHU SINGLA wrote:
> I am trying to learn protein ligand simulation. I tried to follow the steps
> for lysozyme using the GROMACS tutorial. I received the following error:
>
> *ERROR 1 {file jz4.itp, line 183]:*
> * No default Proper Dih. types*
>
>
> *ERROR 2 [file jz4.itp, line 194]:*
> * No default Proper Dih. types*
>
> *Fatal error: *
> *Syntax error -File forcefield.itp, line 10*
> *Last line resd:*
> *'[defaults]'*
> *Invalid order for directive defaults*
>
> Please help me resolve this error.

A [defaults] directive corresponds to the master equations used by the 
simulation and can only appear once, as the first directive in any 
topology (typically it is held in forcefield.itp). Apparently you have 
#include statements out of order. Note that my tutorial tells you 
exactly where to place the relevant #include statements, which will also 
rectify the missing parameter errors.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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