AMBER Archive (2009)

Subject: [AMBER] ambr parameter file creation and usage

From: Donald Keidel (dkeidel_at_scripps.edu)
Date: Tue Nov 03 2009 - 22:39:38 CST

Hi,

I have created the following attached 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 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



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