[gmx-users] How can I convert psf file to top

[Justin Lemkul]

On 4/20/18 12:04 PM, 1185201182 wrote:
> Hi everyone
> I am new to Gromacs. I have generated pdb and psf for my system. And I want to convert it to .top file. I have tried "topo writegmxtop" in vmd using "topo writegmxtop my.top  [list parameterfile1.prm]".   The angles and dihedrals are correct, but the  "type" column in atoms  directive is same as the "atom" column (I mean C1, C2 are the labels for  the "atom", but it should be same label as the one in the forcefiled in  the "type" column ,but it is not in my case). The atom type is already  in my psf file and there is no errors and warnings during the conversion.
>
> Then tried Parmed with following commands:
>
> import parmed as pmd
>   psf=pmd.load_file('AFM_noforcefiled.psf')
>   psf.save('gromacs.top')
>   
> But my linux system is stuck (mouse is locked and changed to  cross-shape,no error messages are reported). And there is no output  after 1 hour(I have about 10000 atoms). And I am able to run the tests  in the test folder before I used above commands.
>
>
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>
>
> My questions are :
>
> (1)Is it a right results from VMD?
>
> (2)What is wrong with my usage of Parmed?
>
> (3)Is there other tool to convert psf to top?
>
> Can any one help me out?

Your questions are not anything to do with GROMACS, so if you're having 
problems with VMD or ParmEd, contact their respective help forums.

-Justin

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

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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