On 5/15/12 12:14 PM, rama david wrote:
Hi Gromacs Friends ..
I am using TFE (Trifluro Ethanol ) as a solvent for my simulation study..
I am using G96 53a6 ff
After the genbox -cp .. -cs tef.pdb -o mix.pdb
I count the no of solvent molecule , to update
topology ..
after Grompp I am facing following error
grompp -f minim.mdp -c mix.pdb -o em.tpr -p final.top
ERROR 1 [file topol-tef.itp, line 46]:
No default Proper Dih. types
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'SOL'
-------------------------------------------------------
Program grompp, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/grompp.c, line: 1372
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I checked the topology for TFE, Dihedral section is as follow ...
*
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
1 2 3 4 1 gd_24
2 3 4 5 1 *
So what to resolve the problem ..
All suggestions are welcome...
The parameters are missing from ffbonded.itp, making the implementation
incomplete. You can obtain a TFE topology from ATB:
http://compbio.biosci.uq.edu.au/atb/download.py?molid=1655
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
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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