[gmx-users] specbonds are not taken by gromos force field?

[Justin Lemkul]

On 4/23/13 9:36 AM, 라지브간디 wrote:
> Dear Justin,
>
>
> Sorry for the confusion.
>
>
> What I was trying to explain is " pdb2gmx output of topol.top file shows the detection of heme (FE) bound with histidine (NE2) atom but missing to mention the gromacs bond, angle, dihedral type code.
>
>
> Which clearly means that pdb2gmx to not able detect the gromacs bond type code to assign their parameters...
>
>
> I have checked the parameter of this heme-his and its found like this :
>
>
> bond
>
>
> #define gb_34        0.198   0.6400e+06
> ; NR  -   FE    120
>
>
> angle
>
> #define ga_17       115.00       50.00; NR(heme)  -  FE  - NR 10
> #define ga_34       125.00      375.00; FE  - NR  - CR1 (5-ring)
> dihedral#define gd_38     0.000        0.0          4; -NR-FE-       0.0
>
> Could you tell how do make pdb2gmx to assign this parameter ? Thanks in advance.
>

If there is a problem with pdb2gmx (i.e. a bug), then you'll have to modify the 
code.  Otherwise, just modify the topology by hand to include the information 
that is missing.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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