AMBER LIBRARIES

I have been foiled in my attempt to build a phosphoserine library for AMBER despite the fact that I know that others seems to have done it. Could anyone 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

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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)
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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.A
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.A Could not find type: o
For atom: .R.A

Could not find type: p5
For atom: .R.A Could not find type: oh
For atom: .R.A Could not find type: ho
For atom: .R.A Could not find type: oh
For atom: .R.A Could not find type: ho
For atom: .R.A Could not find type: os
For atom: .R.A Could not find type: c3
For atom: .R.A Could not find type: h1
For atom: .R.A Could not find type: h1
For atom: .R.A Could not find type: c3
For atom: .R.A Could not find type: n2
For atom: .R.A Could not find type: h
For atom: .R.A Could not find type: h1
For atom: .R.A Could not find type: c
For atom: .R.A 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.

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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.

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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.

# posted by xcrabturtle : 6:37 AM