On 9/09/2011 8:05 AM, Sandeep Somani wrote:
Hi
I am trying to set up a simulation for dialanine using charmm27 ff but
am getting errors in pdb2gmx due to missing definitions in rtp file.
I created the pdb file (below) using Charmm for the sequence
ACE-ALA-ALA-CT3.
pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE
and CT3.
Yes, CHARMM in GROMACS has lacked these for some time. I asked over a
year ago for them to be added, but that hasn't happened. You can add
[ ACE ]
[ atoms ]
CT3 CT3 -0.270 0
HT1 HA 0.090 1
HT2 HA 0.090 2
HT3 HA 0.090 3
C C 0.510 4
O O -0.510 5
[ bonds ]
C CT3
C +N
CT3 HT31
CT3 HT32
CT3 HT33
O C
[ impropers ]
C CT3 +N O
[ CT3 ]
; this can also be done with the .c.tdb, but the atom naming is different
; and this can matter
[ atoms ]
N NH1 -0.470 0
HN H 0.310 1
CT CT3 -0.110 2
HT1 HA 0.090 3
HT2 HA 0.090 4
HT3 HA 0.090 5
[ bonds ]
-C N
N HN
N CAT
CT HT1
CT HT2
CT HT3
[ impropers ]
N -C CAT HN
-C CAT N -O
to the end of aminoacids.rtp in a local copy of the charmm27.ff folder
to make this work.
Does someone have the appropriate definitions for these residues ?
( I have tried http://swissparam.ch/ to generate an itp file for the
molecule, but upon using it in GMX it does not give the same energy as
that from charmm. )
That will likely be a separate issue.
Mark
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