AMBER Archive (2004)

Subject: Re: AMBER: phosphoserine library component

From: Jiten (jiten_at_postech.ac.kr)
Date: Fri Sep 24 2004 - 09:25:24 CDT

Hello,

Instaed of you trying to modify the core files. Please check what are the
missing force field parameters using parmchk

Then you know what to assign for the missing force field parameters by
checking the core files (parm99.dat and gaff.dat.)

If possible use atomtype command to assign proper amber atom type (instead
of gaff atom type) to the atoms of the molecule. ( You need to check
visually again for your satisfaction though)

I hope it helps,

Jiten

----- Original Message -----
From: <jwcraft_at_uh.edu>
To: "Help Amber" <amber_at_scripps.edu>
Sent: Friday, September 24, 2004 11:01 PM
Subject: AMBER: phosphoserine library component

> 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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