AMBER Archive (2009)

Subject: [AMBER] amber parameter file creation and usage

From: Donald Keidel (dkeidel_at_scripps.edu)
Date: Tue Nov 03 2009 - 22:47:36 CST

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

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber