[gmx-users] dihedral format in top file?

[Dallas Warren]

Section 5.3.3 of the manual.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Markus K. Dahlgren
> Sent: Wednesday, 7 December 2011 4:47 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] dihedral format in top file?
> 
> Hi,
> 
> I am inexperienced with gromacs and I would like to figure out the
> format of all
> parts of a .top file, needed for Gromacs. I am trying to understand the
> input
> format so I can write a program for automatic setup for small molecule
> ligands
> with Gromacs, using the oplsaa force field. I have recently written a
> C++
> program that converts BOSS autoput and creates NAMD input. Now I would
> like to
> do a similar program for Gromacs.
> 
> I would like to write as few files as possible. I have some problems
> understanding the format of the dihedrals in the .top file. I have
> pasted the
> top file for methanol I have been preparing manually below. Please
> point out
> any errors. Any pointers would be greatly appreciated.
> 
> Methanol    4
> 
> [atoms]
> 1  opls_157  1  UNK  C00  1  -0.043617
> 2  opls_154  1  UNK  O01  1  -0.586987
> 3  opls_156  1  UNK  H02  1   0.074589
> 4  opls_156  1  UNK  H03  1   0.074589
> 5  opls_156  1  UNK  H04  1   0.074589
> 6  opls_155  1  UNK  H05  1   0.406836
> 
> [bonds]
> 1  2  1  0.14100  267776.00
> 2  6  1  0.09450  462750.40
> 1  2  1  0.14100  284512.00
> 1  2  1  0.14100  284512.00
> 1  2  1  0.14100  284512.00
> 
> [angles]
> 4  1  2   1  109.50  292.880
> 5  1  2   1  109.50  292.880
> 6  2  1   1  108.50  460.240
> 3  1  2   1  109.50  292.880
> 4  1  5   1  107.80  276.144
> 5  1  3   1  107.80  276.144
> 5  1  4   1  107.80  276.144
> 
> [dihedrals]
> 6  2  1  3   3   ??
> ...              ??
> 
> 
> 
> If I want to add the 6-2-1-3 parameter in Ryckaert Bellman format, how
> do I
> enter the information in the dihedral part of the .top file? The RB
> parameters
> for 6-2-1-3 is given below:
> 
> C0 = 0.94140
> C1 = 2.82420
> C2 = 0.00000
> C3 = -3.76560
> C4 = 0.00000
> C5 = 0.00000
> 
> How do I enter this information into the .top file?
> 
> Any help would be greatly appreciated!
> 
> Thanks!
> Best,
> Markus
> 
> 
> 
> 
> 
> 
> 
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists