AMBER Archive (2003)

Subject: force field parameters for phosphoserine

From: Christoph Kluck (christoph.kluck_at_biochemie.uni-freiburg.de)
Date: Tue Apr 29 2003 - 09:07:59 CDT

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