shahid nayeem wrote:
HI
I am using Cytochrome-C pdb 1hrc.pdb. In pdb2gmx it does not gives
any eror using ffG43a1. .top file produced shows all bonds (Fe SD of
MET 80 and Fe NE2 of HIS 18) using spec.dat file but all the error
lines does not have bond/angle nomenclature such as
809 810
HI
I am using Cytochrome-C pdb 1hrc.pdb. In pdb2gmx it does not gives
any eror using ffG43a1. .top file produced shows all bonds (Fe SD of
MET 80 and Fe NE2 of HIS 18) using spec.dat file but all the error
lines does not have bond/angle nomenclature such as
809 810 2gb_30
810
Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
4. grompp -c
shahid nayeem wrote:
Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro
Hi Justin
These errors are from bond between MET/HIS residue and Heme group of
my protein. I checked for all these nine errors of bond and angle in
th file ffG43a1bon.itp and I couldnt find these defined in this file.
Using other options of force field also gives error at some point.
waiting for
shahid nayeem wrote:
Hi Justin
These errors are from bond between MET/HIS residue and Heme group of
my protein. I checked for all these nine errors of bond and angle in
th file ffG43a1bon.itp and I couldnt find these defined in this file.
Using other options of force field also gives error
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