AMBER Archive (2004)

Subject: AMBER: AMBER7 plastocyanin tutorial problem.

From: tarek mahfouz (tmahfouz_at_yahoo.com)
Date: Fri Aug 06 2004 - 12:40:33 CDT

Hi all,

I'm a new user of AMBER and I'm trying to run the plastocyanin tutorial and here is what I did:

1- I prepared the required input files hicu.in and mem.in. However, since later on in the leap.in input file the call is for mem.lib and hicu.lib, I saved hicu.in as hicu.lib and mem.in as mem.lib. They were read ok.

2- I edited the pdb file as explained and run protonate with no complains. The problem comes when I read in the pdb file I get the following messages:

 

> PARM94 = loadamberparams frcmod.pcy
Loading parameters: ./frcmod.pcy
Reading force field mod type file (frcmod)
> plc = loadpdb 1PLC_nowat_h.pdb
Loading PDB file: ./1PLC_nowat_h.pdb
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CE-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CG-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CG-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CE-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CG-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CG-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CG-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CE-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
  total atoms in file: 1443

Now I do not know whats wrong here? Is it the problem with SD? and how to fix this?

 

Also, when I save the prmtop and prmcrd files I get the following message:

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <HIC 37>: -M CA N H
 <HIC 37>: CA +M C O
 <HIC 37>: CE1 CD2 NE2 HE2
 <HIC 37>: CG NE2 CD2 HD2
 <HIC 37>: ND1 NE2 CE1 HE1
 <HIC 37>: ND1 CD2 CG CB
 <MEM 92>: -M CA N H
 <MEM 92>: CA +M C O
 total 288 improper torsions applied
 8 improper torsions in old prep form
Building H-Bond parameters.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res total affected

        CASN 1
        NILE 1
  )
 (no restraints)
and I'm concerned about the statement "residue lacking connect0/connect1" does it mean it will not save the N and C termini as charged?

One more question please, I have a ZN atom in a different pdb file, how to get parameters for this ZN?

Thanks for your help.

Tarek

                
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