On 14/04/2011 5:59 PM, hui sun wrote:
Dear all,
I am having the troubles to obtain the topology file for Cytochrome
C. When I used the Gromos96 53a6 force filed in the GROMACS
4.0.7 software package, the topology file is produced, but there is
lack of some force field parameters, such as the bonds from Cys 14
and Cys 17 to the porphyrin ring and to hold the ligands (Met 80 and
His 18) bound to the heme iron, in this file. When I used the Gromos96
53a6 force filed in the GROMACS 4.5.1 software package, there's a
fatal error: Residue 'HEM' not found in residue topology database. I
have checked the rtp file, in which there is the "HEME" residue.
"HEM" will not always be considered the same as "HEME" by a computer
algorithm... If they're meant to match, name them the same thing in each
place.
Mark
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