AMBER Archive (2009)

Subject: Re: [AMBER] amber parameter file creation and usage

From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Nov 03 2009 - 23:29:30 CST

Hello,

The error messages tell you exactly what's happening. The PDB doesn't make
much sense before the TER card (all I see are hydrogens), so I'll just
assume that whatever comes before that causes the PDB to make sense. The
problem is that you are confusing atom NAMES with atom TYPES in your PDB.
In the PDB, each atom should be given its NAME, not its TYPE. Instead of
having the atoms be labeled NT, CT, CT, SO, O, O, C, O, H1, H1, HS, H, H,
H1, HA, have them labeled by the name given to them in the library file.
(First column are names, second are types). This would be N, C, C1, S, O,
O1, C2, O2, H, H1, H2, H3, H4, H5, H6. It was complaining because several
of these atoms are given the same NAME in the pdb (H and H1 have the same
TYPE, but different NAMES). Replacing the atom TYPES with atom NAMES in the
pdb should be able to make your prmtop file.

However, the frcmod file is warning you in several instances. Parmchk,
which I believe you used to create your frcmod file, looks through a
parameter database for relevant parameters to add. If there's a parameter
that exists in your molecule (for example, an S-O bond between types O and
SO), and it can't find a sensible substitute in the parameter database, it
inserts a line and zeroes all of the parameters, saying "ATTN, needs
revision". Thus, if you use any prmtop created by that frcmod, you will
certainly get wrong results. Thus, for each line in the frcmod file that
says "ATTN, needs revision", you need to find (or calculate) the appropriate
parameter. There are several other threads in which people have posted
locations of custom parameters, so you can search the mailing list for these
instances. As it stands right now, though, your frcmod should not be used
to create a topology file that you use in simulations.

Good luck!
Jason

On Tue, Nov 3, 2009 at 11:47 PM, Donald Keidel <dkeidel_at_scripps.edu> wrote:

> Hi,
>
> I have created the following files:
>
> 1. SOC_amber.frcmod
> 2. SOC_amber.lib
> 3. SOC_Min1_amber.prepi
>
>
> Using tutorials I have used before that I was successful with on other
> small molecules.
>
> I could not attach them even if I zipped them so I have pasted them at the
> bottom of this email. The complete pdb is not attched, only the relevant
> coordinates.
>
> I load the the .lib and frcmod into tleap along with a pdb that has what I
> think are correct corresponding types.
>
> I execute the following commands in tleap:
>
> tleap
>
> > loadoff SOC_amber.lib
> Loading library: ./SOC_amber.lib
> > loadamberparams SOC_amber.frcmod
> Loading parameters: ./SOC_amber.frcmod
> Reading force field modification type file (frcmod) Reading title:
> remark goes here
> > prot= loadPdb 2SNI_r_u_TERENDFH_cyx_his.pdb
> Loading PDB file: ./2SNI_r_u_TERENDFH_cyx_his.pdb
> -- residue 275: duplicate [ CT] atoms (total 2)
> -- residue 275: duplicate [ H] atoms (total 2)
> -- residue 275: duplicate [ H1] atoms (total 3)
> -- residue 275: duplicate [ O] atoms (total 3)
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
> Added missing heavy atom: .R<CGLN 274>.A<OXT 18>
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported ---Tried to
> +superimpose torsions for: *-C1-S-*
> +--- With Sp3 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> Created a new atom named: NT within residue: .R<SOC 275> Created a new atom
> named: CT within residue: .R<SOC 275> Created a new atom named: SO within
> residue: .R<SOC 275> Created a new atom named: HS within residue: .R<SOC
> 275> Created a new atom named: HA within residue: .R<SOC 275>
> Added missing heavy atom: .R<SOC 275>.A<N 1>
> Added missing heavy atom: .R<SOC 275>.A<C1 3>
> Added missing heavy atom: .R<SOC 275>.A<C2 7>
> Added missing heavy atom: .R<SOC 275>.A<S 4>
> Added missing heavy atom: .R<SOC 275>.A<O2 8>
> Added missing heavy atom: .R<SOC 275>.A<O1 6>
> total atoms in file: 3840
> Leap added 13 missing atoms according to residue templates:
> 7 Heavy
> 6 H / lone pairs
> The file contained 5 atoms not in residue templates
> > saveAmberParm prot 2SNI_r_u_ToMin.top 2SNI_r_u_ToMin.crd
> Checking Unit.
> WARNING: There is a bond of 3.141250 angstroms between:
> ------- .R<THR 220>.A<C 13> and .R<MET 221>.A<N 1>
> WARNING: There is a bond of 4.802990 angstroms between:
> ------- .R<SOC 275>.A<C1 3> and .R<SOC 275>.A<H 9>
> WARNING: There is a bond of 3.352835 angstroms between:
> ------- .R<SOC 275>.A<C1 3> and .R<SOC 275>.A<H1 10>
> WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
> WARNING: The perturbed charge: -1.000001 is not zero.
> FATAL: Atom .R<SOC 275>.A<NT 16> does not have a type.
> FATAL: Atom .R<SOC 275>.A<CT 17> does not have a type.
> FATAL: Atom .R<SOC 275>.A<SO 18> does not have a type.
> FATAL: Atom .R<SOC 275>.A<HS 19> does not have a type.
> FATAL: Atom .R<SOC 275>.A<HA 20> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
>
>
>
> I get these FATAL warnings that I am not too sure why they appear in the
> first place. I have looked at the .inp and frcmod files and as far as I can
> see these atom types have been defined with forcefeild parameters.
>
> I am turning to the amber mailing list since it is not clear to me how this
> can occur.
>
> I appreciate all help and look forward to any responses.
>
> Thank you
>
> Don Keidel
>
>
>
>
> .lib file:
>
> !!index array str
> "SOC"
> !entry.SOC.unit.atoms table str name str type int typex int resx int
> flags int seq int elmnt dbl chg
> "N" "NT" 0 1 131075 1 7 0.0
> "C" "CT" 0 1 131075 2 6 0.0
> "C1" "CT" 0 1 131075 3 6 0.0
> "S" "SO" 0 1 131075 4 16 0.0
> "O" "O" 0 1 131075 5 8 0.0
> "O1" "O" 0 1 131075 6 8 0.0
> "C2" "C" 0 1 131075 7 6 0.0
> "O2" "O" 0 1 131075 8 8 0.0
> "H" "H1" 0 1 131075 9 1 0.0
> "H1" "H1" 0 1 131075 10 1 0.0
> "H2" "HS" 0 1 131075 11 1 0.0
> "H3" "H" 0 1 131075 12 1 0.0
> "H4" "H" 0 1 131075 13 1 0.0
> "H5" "H1" 0 1 131075 14 1 0.0
> "H6" "HA" 0 1 131075 15 1 0.0
> !entry.SOC.unit.atomspertinfo table str pname str ptype int ptypex int
> pelmnt dbl pchg
> "N" "NT" 0 -1 -0.979650
> "C" "CT" 0 -1 0.391374
> "C1" "CT" 0 -1 -0.507566
> "S" "SO" 0 -1 0.863455
> "O" "O" 0 -1 -0.479112
> "O1" "O" 0 -1 -0.479112
> "C2" "C" 0 -1 0.392243
> "O2" "O" 0 -1 -0.424901
> "H" "H1" 0 -1 0.184693
> "H1" "H1" 0 -1 0.184693
> "H2" "HS" 0 -1 0.054947
> "H3" "H" 0 -1 0.378500
> "H4" "H" 0 -1 0.378500
> "H5" "H1" 0 -1 0.030276
> "H6" "HA" 0 -1 0.011659
> !entry.SOC.unit.boundbox array dbl
> -1.000000
> 0.0
> 0.0
> 0.0
> 0.0
> !entry.SOC.unit.childsequence single int
> 2
> !entry.SOC.unit.connect array int
> 0
> 0
> !entry.SOC.unit.connectivity table int atom1x int atom2x int flags
> 1 2 1
> 1 13 1
> 1 12 1
> 2 3 1
> 2 7 1
> 2 14 1
> 3 4 1
> 3 9 1
> 3 10 1
> 4 5 1
> 4 11 1
> 4 6 1
> 7 15 1
> 7 8 1
> !entry.SOC.unit.hierarchy table str abovetype int abovex str belowtype
> int belowx
> "U" 0 "R" 1
> "R" 1 "A" 1
> "R" 1 "A" 2
> "R" 1 "A" 3
> "R" 1 "A" 4
> "R" 1 "A" 5
> "R" 1 "A" 6
> "R" 1 "A" 7
> "R" 1 "A" 8
> "R" 1 "A" 9
> "R" 1 "A" 10
> "R" 1 "A" 11
> "R" 1 "A" 12
> "R" 1 "A" 13
> "R" 1 "A" 14
> "R" 1 "A" 15
> !entry.SOC.unit.name single str
> ""
> !entry.SOC.unit.positions table dbl x dbl y dbl z
> 12.620000 -4.114000 9.406000
> 12.866000 -2.722000 9.686000
> 13.066000 -1.904000 8.373000
> 13.638000 -2.652000 6.775000
> 12.436000 -2.021000 5.718000
> 13.301000 -4.323000 6.612000
> 11.690000 -2.134000 10.454000
> 11.892000 -1.134000 11.135000
> 12.045000 -1.551000 8.226000
> 13.839000 -1.213000 8.710000
> 14.925000 -2.474000 6.544000
> 11.672000 -4.450000 9.308000
> 13.395000 -4.754000 9.308000
> 13.769000 -2.732000 10.296000
> 10.648000 -2.446000 10.520000
> !entry.SOC.unit.residueconnect table int c1x int c2x int c3x int c4x
> int c5x int c6x
> 0 0 0 0 0 0
> !entry.SOC.unit.residues table str name int seq int childseq int
> startatomx str restype int imagingx
> "SOC" 1 16 1 "?" 0
> !entry.SOC.unit.residuesPdbSequenceNumber array int
> 1
> !entry.SOC.unit.solventcap array dbl
> -1.000000
> 0.0
> 0.0
> 0.0
> 0.0
> !entry.SOC.unit.velocities table dbl x dbl y dbl z
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
> 0.0 0.0 0.0
>
>
> Frcmod file:
>
> remark goes here
> MASS
> O 16.000 0.434 same as o
> SO 0.000 0.000 ATTN, need revision
> HS 1.008 0.135 same as hs
> CT 12.010 0.878 same as c3
> H1 1.008 0.135 same as hc
> NT 14.010 0.530 same as n3
> H 1.008 0.161 same as hn
> C 12.010 0.616 same as c
> HA 1.008 0.135 same as hc
>
> BOND
> O -SO 0.00 0.000 ATTN, need revision
> SO-HS 0.00 0.000 ATTN, need revision
> SO-CT 0.00 0.000 ATTN, need revision
> CT-H1 337.30 1.092 same as c3-hc
> CT-CT 303.10 1.535 same as c3-c3
> CT-NT 320.60 1.470 same as c3-n3
> CT-C 328.30 1.508 same as c -c3
> NT-H 394.10 1.018 same as hn-n3
> C -HA 0.00 0.000 ATTN, need revision
> C -O 648.00 1.214 same as c -o
>
> ANGLE
> O -SO-O 0.000 0.000 ATTN, need revision
> O -SO-HS 0.000 0.000 ATTN, need revision
> O -SO-CT 0.000 0.000 ATTN, need revision
> SO-CT-H1 0.000 0.000 ATTN, need revision
> SO-CT-CT 0.000 0.000 ATTN, need revision
> HS-SO-CT 0.000 0.000 ATTN, need revision
> CT-CT-NT 66.200 110.380 same as c3-c3-n3
> CT-CT-H1 46.400 110.050 same as c3-c3-hc
> CT-CT-C 63.800 110.530 same as c -c3-c3
> H1-CT-H1 39.400 108.350 same as hc-c3-hc
> CT-NT-H 47.100 109.920 same as c3-n3-hn
> CT-C -HA 0.000 0.000 ATTN, need revision
> CT-C -O 68.000 123.110 same as c3-c -o
> NT-CT-H1 49.400 109.800 same as hc-c3-n3
> NT-CT-C 65.800 113.910 same as c -c3-n3
> H -NT-H 41.300 107.130 same as hn-n3-hn
> H1-CT-C 47.200 109.680 same as c -c3-hc
> HA-C -O 55.400 120.000 same as hc-c -o
>
> DIHE
> O -SO-CT-H1 1 0.000 0.000 0.000 ATTN, need
> revision
> O -SO-CT-CT 1 0.000 0.000 0.000 ATTN, need
> revision
> SO-CT-CT-NT 1 0.000 0.000 0.000 ATTN, need
> revision
> SO-CT-CT-H1 1 0.000 0.000 0.000 ATTN, need
> revision
> SO-CT-CT-C 1 0.000 0.000 0.000 ATTN, need
> revision
> HS-SO-CT-H1 1 0.000 0.000 0.000 ATTN, need
> revision
> HS-SO-CT-CT 1 0.000 0.000 0.000 ATTN, need
> revision
> CT-CT-NT-H 1 0.300 0.000 3.000 same as X
> -c3-n3-X
> CT-CT-C -HA 1 0.000 180.000 2.000 same as X -c
> -c3-X
> CT-CT-C -O 1 0.000 180.000 2.000 same as X -c
> -c3-X
> H1-CT-CT-NT 1 0.156 0.000 3.000 same as X
> -c3-c3-X
> H1-CT-CT-H1 1 0.150 0.000 3.000 same as
> hc-c3-c3-hc
> H1-CT-CT-C 1 0.156 0.000 3.000 same as X
> -c3-c3-X
> NT-CT-C -HA 1 0.000 180.000 2.000 same as X -c
> -c3-X
> NT-CT-C -O 1 0.000 180.000 2.000 same as X -c
> -c3-X
> H -NT-CT-H1 1 0.300 0.000 3.000 same as X
> -c3-n3-X
> H -NT-CT-C 1 0.300 0.000 3.000 same as X
> -c3-n3-X
> H1-CT-C -HA 1 0.000 180.000 2.000 same as X -c
> -c3-X
> H1-CT-C -O 1 0.800 0.000 -1.000 same as hc-c3-c
> -o
> H1-CT-C -O 1 0.080 180.000 3.000 same as hc-c3-c
> -o
>
> IMPROPER
> CT-HA-C -O 1.1 180.0 2.0 Using default
> value
>
> NONBON
> O 1.6612 0.2100 same as o
> SO 0.0000 0.0000 ATTN, need revision
> HS 0.6000 0.0157 same as hs
> CT 1.9080 0.1094 same as c3
> H1 1.4870 0.0157 same as hc
> NT 1.8240 0.1700 same as n3
> H 0.6000 0.0157 same as hn
> C 1.9080 0.0860 same as c
> HA 1.4870 0.0157 same as hc
>
>
> Coordinates from the pdb file used:
>
> .
> .
> .
> ATOM 0 H GLN A 275 10.399 -6.157 33.952 1.00 20.40
> H new
> ATOM 0 HA GLN A 275 10.331 -6.646 36.146 1.00 24.09
> H new
> ATOM 0 HB2 GLN A 275 13.068 -5.364 35.790 1.00 26.61
> H new
> ATOM 0 HB3 GLN A 275 12.554 -6.041 37.341 1.00 26.61
> H new
> ATOM 0 HG2 GLN A 275 12.294 -8.274 36.236 1.00 35.29
> H new
> ATOM 0 HG3 GLN A 275 12.916 -7.573 34.737 1.00 35.29
> H new
> ATOM 0 HE21 GLN A 275 16.176 -8.271 35.674 1.00 43.93
> H new
> ATOM 0 HE22 GLN A 275 14.890 -8.408 34.521 1.00 43.93
> H new
> TER
> HETATM 1 NT SOC 1 12.620 -4.114 9.406 1.00 0.00
> HETATM 2 CT SOC 1 12.866 -2.722 9.686 1.00 0.00
> HETATM 3 CT SOC 1 13.066 -1.904 8.373 1.00 0.00
> HETATM 4 SO SOC 1 13.638 -2.652 6.775 1.00 0.00
> HETATM 5 O SOC 1 12.436 -2.021 5.718 1.00 0.00
> HETATM 6 O SOC 1 13.301 -4.323 6.612 1.00 0.00
> HETATM 7 C SOC 1 11.690 -2.134 10.454 1.00 0.00
> HETATM 8 O SOC 1 11.892 -1.134 11.135 1.00 0.00
> HETATM 9 H1 SOC 1 12.045 -1.551 8.226 1.00 0.00
> HETATM 10 H1 SOC 1 13.839 -1.213 8.710 1.00 0.00
> HETATM 11 HS SOC 1 14.925 -2.474 6.544 1.00 0.00
> HETATM 12 H SOC 1 11.672 -4.450 9.308 1.00 0.00
> HETATM 13 H SOC 1 13.395 -4.754 9.308 1.00 0.00
> HETATM 14 H1 SOC 1 13.769 -2.732 10.296 1.00 0.00
> HETATM 15 HA SOC 1 10.648 -2.446 10.520 1.00 0.00
> TER
> END
>
> _______________________________________________
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> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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