[gmx-users] Re: How to add dihedral information from the GAFF topology

[Justin A. Lemkul]

Biswajit Gorai wrote:
> Dear Bipin,
> Edit your topology file as:
> 
> ###########################################
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
> 
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Ion_chain_A2.itp"
> 
> *#include "oct.itp"*
> 

If oct.itp introduces new atom types (as the original .top does, for GAFF), 
placing this topology here will result in a fatal error since there is a new 
[atomtypes] directive that is introduced after the protein [moleculetype].  If 
oct.itp does not introduce any new atom types, its location within the system 
topology is irrelevant.

> ; Include water topology
> #include "amber99sb-ildn.ff/tip3p.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>   1    1       1000       1000       1000
> #endif
> 
> ; Include topology for ions
> #include "amber99sb-ildn.ff/ions.itp"
> 
> [ system ]
> ; Name
> Protein in water
> 
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Ion_chain_A2        1
> *1-octanol         1
> *
> *SOL              8987*

Depending on the order of the coordinate file, it may not be possible to merge 
the SOL entries in this way.

-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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