AMBER Archive (2004)

Subject: AMBER: phosphoserine library component

From: jwcraft_at_uh.edu
Date: Fri Sep 24 2004 - 09:01:28 CDT

Dear Sirs,

I have been foiled in my attempt to build a phosphoserine library for
AMBER despite the fact that I know that others seem to have done it.
Could you comment one my strategy to build this library? I am sure I
am close, but ... you know how working with code that you are just
learning goes.... anyway I would also like to know the relationships
between the many library files as well, as my misunderstanding might be
at the root cause of my errors.

Here is what I did.

1) Build the residue in Insight, used its optimization to relax the
molecule to get appropriate bond angles, and lengths
2) Run antechamber to get a sep.prepin library fragment to use in tleap
3) Goal: Run tleap to generate a general prmtop file for the AMBER
molecular simulation
4) Goal: Run sander

----------------------------------
Result of 2:
     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 O2P o S 3 2 1 1.540 111.208 180.000 0.000
    5 P p5 S 4 3 2 1.592 70.512 -161.384 0.000
    6 O1P oh S 5 4 3 1.535 109.613 -116.390 0.000
    7 H1P ho E 6 5 4 0.958 104.360 -50.138 0.000
    8 O3P oh S 5 4 3 1.536 110.667 124.265 0.000
    9 H3P ho E 8 5 4 0.955 104.575 174.086 0.000
   10 OG os S 5 4 3 1.615 109.785 3.781 0.000
   11 CB c3 S 10 5 4 1.450 122.662 56.061 0.000
   12 HB2 h1 E 11 10 5 1.111 110.009 65.687 0.000
   13 HB3 h1 E 11 10 5 1.111 109.974 -48.967 0.000
   14 CA c3 M 11 10 5 1.546 111.429 -171.456 0.000
   15 N n2 M 14 11 10 1.494 108.382 55.875 0.000
   16 HN h E 15 14 11 1.031 108.234 -55.713 0.000
   17 HA h1 E 14 11 10 1.109 107.616 173.545 0.000
   18 C c M 14 11 10 1.558 111.435 -71.121 0.000
   19 O o E 18 14 11 1.224 122.962 -99.193 0.000

LOOP

IMPROPER

DONE
STOP

This seems to be ok, I had solved a number of geometry problems and
nomenclature problems last week and the data seems resonable. However,
I had to hand edit this file because the original antechamber output
kept calling PO(4-) atoms M for main backbone and not S for sidechain
(maybe a sign that I have done this wrong too)
----------------------------------------------
Result of 3:
Loading Prep file: ./sep.prepin
Loading parameters: ./frcmod
Reading force field mod type file (frcmod)
Loading PDB file: ./leap_temp_pro.apdb
   Added missing heavy atom: .R<CSER 19>.A<OXT 12>
   total atoms in file: 290
   Leap added 3 missing atoms according to residue templates:
        1 Heavy
        2 H / lone pairs
Checking Unit.
WARNING: The unperturbed charge of the unit: 2.000000 is not zero.

  -- ignoring the warning.

Building topology.
Building atom parameters.
For atom: .R<SEP 9>.A<O2P 1> Could not find type: o
For atom: .R<SEP 9>.A<P 2> Could not find type: p5
For atom: .R<SEP 9>.A<O1P 3> Could not find type: oh
For atom: .R<SEP 9>.A<H1P 4> Could not find type: ho
For atom: .R<SEP 9>.A<O3P 5> Could not find type: oh
For atom: .R<SEP 9>.A<H3P 6> Could not find type: ho
For atom: .R<SEP 9>.A<OG 7> Could not find type: os
For atom: .R<SEP 9>.A<CB 8> Could not find type: c3
For atom: .R<SEP 9>.A<HB2 9> Could not find type: h1
For atom: .R<SEP 9>.A<HB3 10> Could not find type: h1
For atom: .R<SEP 9>.A<CA 11> Could not find type: c3
For atom: .R<SEP 9>.A<N 12> Could not find type: n2
For atom: .R<SEP 9>.A<HN 13> Could not find type: h
For atom: .R<SEP 9>.A<HA 14> Could not find type: h1
For atom: .R<SEP 9>.A<C 15> Could not find type: c
For atom: .R<SEP 9>.A<O 16> Could not find type: o
Parameter file was not saved.

But the problem seems to be with the names O, P5, OH, etc and that is
what antechamber produced! I then looked through files like

all_amino94.lib all_amino02.lib
parm94.dat
all_amino94.in

I tried capitalization, renaming, etc and been lead astray by things
like the fact the _every_ standard residue had a nitrogen - hydrogen
label H and leap _wouldnot_ take that for my new residue ... it wanted
to be labeled HN. Why, I am not sure but presumably there is a list of
aliases from H -> HN for predefined residues.

-----------------------
Then I tried to modify the core library directly, that is
all_amino94.lib That is almost complete, but apparently the section :

!entry.SER.unit.positions table dbl x dbl y dbl z
  3.325770 1.547909 -1.607257E-06
  3.909407 0.723611 -2.739904E-06
  3.970048 2.845795 -1.312144E-07
  3.671663 3.400129 -0.889820
  3.576965 3.653838 1.232143
  2.496995 3.801075 1.241379
  3.877484 3.115795 2.131197
  4.230753 4.925145 1.196917
  3.983305 5.433814 1.972562
  5.485541 2.705207 -4.398851E-06
  6.008824 1.593175 -8.449829E-06

as a tempate for my new !entry SEP ...

needs to have the HN-N-CA-C in a plane and so am I making that
transformation. When I place a general set of coordinated in leap said
that the file was not a valid library.

----------------------

Am I following the process correctly? As a minor note I have been able
to build libraries for both Dyana and MolMol and they are working. Any
comments would be greatly appreciated.

Thank You Very Much

JWCraft

John W. Craft, Jr.
University of Houston
http://accesstospace.blogspot.com

 From Dr. Legge's Lab

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