On 4/23/13 9:36 AM, 라지브간디 wrote:
Dear Justin,
Sorry for the confusion.
What I was trying to explain is " pdb2gmx output of topol.top file shows the
detection of heme (FE) bound with histidine (NE2) atom but missing to mention the
gromacs bond, angle, dihedral type code.
Which clearly means that pdb2gmx to not able detect the gromacs bond type code
to assign their parameters...
I have checked the parameter of this heme-his and its found like this :
bond
#define gb_34 0.198 0.6400e+06
; NR - FE 120
angle
#define ga_17 115.00 50.00; NR(heme) - FE - NR 10
#define ga_34 125.00 375.00; FE - NR - CR1 (5-ring)
dihedral#define gd_38 0.000 0.0 4; -NR-FE- 0.0
Could you tell how do make pdb2gmx to assign this parameter ? Thanks in advance.
If there is a problem with pdb2gmx (i.e. a bug), then you'll have to modify the
code. Otherwise, just modify the topology by hand to include the information
that is missing.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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