On 9/13/12 4:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
this atom is the CG atom of the phosphate I added to the protein.
But how can I find out by what it is punished?
Visualization.
This is the topology for this residue in the aminoacid.rtp file. I added
it manually. The parameter are from the amber parameter database
(http://www.pharmacy.manchester.ac.uk/bryce/amber/):
[ TYP ]
[ atoms ]
N N -0.516300 1
CA CT 0.275503 2
HA H1 0.008223 3
CB CT -0.354052 4
HB1 HC 0.110326 5
HB2 HC 0.110326 6
CG CA 0.119728 7
CD1 CA -0.198938 8
HD1 HA 0.137143 9
CE1 CA -0.284884 10
HE1 HA 0.177179 11
CZ C 0.452616 12
OH OS -0.534452 13
H H 0.293600 14
CE2 CA -0.284884 15
HE2 HA 0.177179 16
CD2 CA -0.198938 17
HD2 HA 0.137143 18
C C 0.536600 19
O O -0.581900 20
P P 1.393213 21
OP1 OH -0.752821 22
OP2 O2 -0.822464 23
OP3 O2 -0.822464 24
H1P HO 0.423316 25
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CE1 HE1
CE1 CZ
CZ OS
CZ CE2
OS P
CE2 HE2
CE2 CD2
CD2 HD2
C O
-C N
P OP1
P OP2
P OP3
OP1 H1P
[ impropers ]
-C CA N H
CA +N C O
CG CE2 CD2 HD2
CZ CD2 CE2 HE2
CD1 CZ CE1 HE1
CG CE1 CD1 HD1
CD1 CD2 CG CB
CE1 CE2 CZ OH
Additionally I had to add an entry in the ffbonded file in the part [
dihedraltypes ]
CA CA C OS 4 180.00 4.60240 2 ;
Here I am not completely sure about the entry because I could not find a
source for this combination of atoms.
But there is already an entry for the combination
CA CA C OH
Which has the same parameters.
Could this be the problem?
And if it could be, can you please give me hint where I can find
parameters for it? Because I really could not find it.
Potentially - if you haphazardly assign parameters, you may get unexpected
results. There is a cited reference for the TYP parameters at the website
above. I would suggest looking there first, and if there is nothing listed,
then contact the corresponding author of the study that first used/derived the
parameters.
Additionally, if you freeze a part of the protein's structure, you prevent any
existing clashes from being resolved. That may be the root of the issue.
-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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