subject: force field parameters for phosphoserine
Dear amber-users,
could anybody provide me the forcefieldparameters for
Phosphoserine (SEP)?
I generated prep and parm file of SEP using antechamber,
but neverthess xleap
is complaining when generating the topology file and
coordinate file for
a peptide containing a SEP:
Could not find bond parameter for: P - O
Could not find bond parameter for: O - P
..
..
Could not find angle parameter: O - P - O
Could not find angle parameter: O - P - O
Building proper torsion parameters.
Building improper torsion parameters.
Did I miss some steps in xleap?
(the commands I did:
loadamberparams parm94.dat
loadoff SEP.lib
a=loadpdb pep.pdb
savepdb a xleap.pdb
a=loadpdb xleap.pdb
saveamberparm a pep.tpp pep.rst
It would be very helpfull if you could give me some hints.
Thanks very much
Christoph
SEP.parm file:
--------------
remark goes here
MASS
BOND
ANGLE
n4-c3-c 65.502 112.450 Calculated with empirical
approach
hx-c3-c 50.000 109.500 same as c -c3-hc
DIHE
IMPROPER
NONBON
SEP.prep file:
--------------
0 0 2
This is a remark line
molecule.res
SEP XYZ 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0
.0 .00000
2 DUMM DU M 1 0 -1 1.449 .0
.0 .00000
3 DUMM DU M 2 1 0 1.522 111.1
.0 .00000
4 O1P o M 3 2 1 1.540 111.208
180.000 -0.236
5 P p5 M 4 3 2 1.497 50.096
170.726 1.350
6 O2P o E 5 4 3 1.487 102.515
-147.525 -0.220
7 O3P o E 5 4 3 1.479 121.492
92.880 -0.646
8 OG os M 5 4 3 1.630 107.567
-30.553 -0.545
9 CB c3 M 8 5 4 1.459 122.177
-165.591 0.219
10 HB1 h1 E 9 8 5 1.089 106.041
5.526 0.058
11 HB2 h1 E 9 8 5 1.090 106.030
118.048 0.087
12 CA c3 M 9 8 5 1.541 112.682
-118.236 -0.087
13 N n4 3 12 9 8 1.454 114.481
-112.250 -0.760
14 HN1 hn E 13 12 9 1.030 109.498
-179.985 0.200
15 HN2 hn E 13 12 9 1.030 109.518
-59.911 0.428
16 HN3 hn E 13 12 9 1.030 109.483
60.036 0.217
17 HA hx E 12 9 8 1.090 107.617
8.108 0.150
18 C c M 12 9 8 1.532 113.304
126.199 0.889
19 OXT o E 18 12 9 1.229 120.486
-129.825 -0.527
20 O o M 18 12 9 1.225 121.282
54.401 -0.575
LOOP
IMPROPER
CA OXT C O
DONE
STOP
Received on Tue Apr 29 2003 - 15:53:01 PDT
