[gmx-users] problem with pdb2gmx to generate top file

[Justin A. Lemkul]

Moeed wrote:
> Hello,
> 
> I am trying to generate gro and top file with pdb2gmx program. I have 
> made a copy of ffoplsaa.rtp from library to working directory and added 
> Hexane molecule residue to the beginning of the ffoplsaa.rtp.
> 
> 
> *****************************************.
> .
> .
> .
> .
> .
> ; Col 4: Type of improper dihedrals
> ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
> ; Col 6: Number of excluded neighbors for nonbonded interactions
> ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1
> ; Col 8: Remove propers over the same bond as an improper if it is 1
> ; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
>      1       1          3          1        1         3      1     0
> 
> [ HEX ]
>  [ atoms ]
>     C1   opls_157    -0.180      1
>     H11  opls_140     0.060      1
>     H12  opls_140     0.060      1
>     H13  opls_140     0.060      1
>     C2   opls_158    -0.120      2
>     H21  opls_140     0.060      2
>     H22  opls_140     0.060      2
>     C3   opls_158     0.120      3
>     H31  opls_140     0.060      3
>     H32  opls_140     0.060      3
>     C4   opls_158    -0.120      4
>     H41  opls_140     0.060      4
>     H42  opls_140     0.060      4
>     C5   opls_158    -0.120      5
>     H51  opls_140     0.060      5
>     H52  opls_140     0.060      5
>     C6   opls_157    -0.180      6
>     H61  opls_140     0.060      6
>     H62  opls_140     0.060      6
>     H63  opls_140     0.060      6
>  [ bonds ]
>     C1   H11
>     C1   H12
>     C1   H13
>     C1   C2
>     C2   H21
>     C2   H22
>     C2   C3
>     C3   H31
>     C3   H32
>     C3   C4
>     C4   H41
>     C4   H42
>     C4   C5
>     C5   H51
> 

Here's a problem (although not one that should cause pdb2gmx to somehow fail). 
You haven't defined any bonds to C5-C6 or C6 to any of its hydrogens.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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