[gmx-users] .hdb---file in gromacs

[Justin Lemkul]

On 7/23/12 2:47 PM, Debashis Sahu wrote:
> Dear all user,
>                    I'm a gromacs beginner and have a quick question.
> Can anyone tell me about the .hdb file description, e.g. '8' indictes
> no.of kind of hydrogen, ARG is residue name, after that 1st column
> indicates the no. of hydrogens for each type but 2nd column's
> indication is not clear to me. And also which basis the atom type are
> mentioned in .hdb file. Here, I given the part of .hdb file for ARG
> residue.
> Please help me

Have you read manual section 5.6.4?  The answers to all of these questions are 
there.

-Justin

>
> ARG     8
> 1      1     H          N          -C           CA
> 1      5     HA       CA         N            C              CB
> 2      6     HB       CB         CG         CA
> 2      6     HG      CG         CD          CB
> 2      6     HD      CD          NE         CG
> 1      1     HE      NE          CD         CZ
> 2      3     HH1    NH1        CZ          NE
> 2      3     HH2    NH2        CZ          NE
>
>
>
> DEBASHIS
>

-- 
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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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