Here is the blocking group from
gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp
KK
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 1
HH32 HA 0.090 2
HH33 HA 0.090 3
C C 0.510 4
O O -0.510 5
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
On 1/6/12 12:40 PM, Peter C. Lai wrote:
Corrected bonds section (sorry been up all night)
[ ACE ]
[ atoms ]
CH3 CT3 -0.27 0
HH31 HA 0.09 1
HH32 HA 0.09 2
HH33 HA 0.09 3
C C 0.51 4
O O -0.51 5
[ bonds ]
CH3 HH31
CH3 HH32
CH3 HH33
CH3 C
C O
Surprisingly, an .hdb entry for ACE exists so you don't need to create one.
(and the .hdb entry uses HH3 as the base hydrogen name in ACE)
On 2012-01-06 12:23:49PM -0600, Peter C. Lai wrote:
Gromos96 53A6 has it.
On 2012-01-06 01:18:38PM -0500, Dariush Mohammadyani wrote:
I tried charmm27 too.
Error:
Residue 'ACE' not found in residue topology database
I tried all forcefield in the list provided by "pdb2gmx", but non of them
works.
Dariush
On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers<rjham...@wisc.edu> wrote:
HEME is in the charmm27 force field.
bob h.
On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote:
Yes, I have PDB file (1HRC.pdb). However, when I try to use "pdb2gmx" I
get this error:
Residue 'HEM' not found in residue topology database
and HEM is Iron ion inside this protein. I do not know which forcefield is
proper to use. I also tried MARTINI force field according their website; I
used martinize.py script; Again I got error.
Regards,
Dariush
On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul<jalem...@vt.edu> wrote:
Dariush Mohammadyani wrote:
Hi all,
Has anybody made initial configuration for Cytochrom C? Can it be shared
with me?
There are several in the PDB.
-Justin
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