AMBER Archive (2004)

Subject: Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file

From: Carsten Detering (detering_at_u.washington.edu)
Date: Fri Mar 05 2004 - 12:19:18 CST

i guess you forgot to load the amber prepfile for you molecule. after
loadamberparms frcmod, you have to loadmaberprep yourfile.prep
hope this helps.

carsten
----- Original Message -----
From: "yonchen" <yonchen_at_ic.sunysb.edu>
To: <amber_at_scripps.edu>
Cc: <yonchen_at_ic.sunysb.edu>
Sent: Thursday, March 04, 2004 5:01 AM
Subject: AMBER: Use tleap convert *.pdb file to *.top and *.crd file

> Dear Carsten and Case:
>
> Thank you for your hints. I edited the original pdb file to make sure
> that atom names are unique and I tried to create a frcmod as following
> method.
>
> antechamber -i bsheettest.pdb -fi pdb -o bsheettest.prep -fo prepi
> parmchk -i bsheettest.prep -f prepi -o frcmod
>
> But I still met the following problems.
>
> [yongzhi_at_dhcp-143-109 exe]$ more frcmod
> remark goes here
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
> c3-c3-ca-ca 1.1 180.0 2.0 Using
> default value
> ca-ca-c3-ha 1.1 180.0 2.0 Using
> default value
> c3-ca-ca-ha 1.1 180.0 2.0 Using
> default value
> ca-ca-ca-ha 1.1 180.0 2.0 Using
> default value
> ca-ca-ca-oh 1.1 180.0 2.0 Using
> default value
> ca-ha-c3-na 1.1 180.0 2.0 Using
> default value
> c3-ca-na-ha 1.1 180.0 2.0 Using
> default value
> ca-ca-ca-na 1.1 180.0 2.0 Using
> default value
> ca-ca-ca-ca 1.1 180.0 2.0 Using
> default value
>
> NONBON
>
> [yongzhi_at_dhcp-143-109 exe]$ tleap
> -I: Adding /home/yongzhi/Documents/amber7/dat/leap/prep to search path.
> -I: Adding /home/yongzhi/Documents/amber7/dat/leap/lib to search path.
> -I: Adding /home/yongzhi/Documents/amber7/dat/leap/parm to search path.
> -I: Adding /home/yongzhi/Documents/amber7/dat/leap/cmd to search path.
>
> Welcome to LEaP!
> (no leaprc in search path)
> > source leaprc.ff99
> ----- Source: /home/yongzhi/Documents/amber7/dat/leap/cmd/leaprc.ff99
> ----- Source of /home/yongzhi/Documents/amber7/dat/leap/cmd/leaprc.ff99
> done
> Log file: ./leap.log
> Loading parameters:
> /home/yongzhi/Documents/amber7/dat/leap/parm/parm99.dat
> Loading library:
> /home/yongzhi/Documents/amber7/dat/leap/lib/all_nucleic94.lib
> Loading library:
> /home/yongzhi/Documents/amber7/dat/leap/lib/all_amino94.lib
> Loading library:
> /home/yongzhi/Documents/amber7/dat/leap/lib/all_aminoct94.lib
> Loading library:
> /home/yongzhi/Documents/amber7/dat/leap/lib/all_aminont94.lib
> Loading library: /home/yongzhi/Documents/amber7/dat/leap/lib/ions94.lib
> Loading library:
> /home/yongzhi/Documents/amber7/dat/leap/lib/solvents.lib
> > loadamberparams frcmod
> Loading parameters: ./frcmod
> Reading force field mod type file (frcmod)
> > bsheettest = loadpdb bsheettest.pdb
> Loading PDB file: ./bsheettest.pdb
> Created a new atom named: HNCA within residue: .R<NVAL 1>
> Created a new atom named: H within residue: .R<NVAL 1>
> Created a new atom named: HG11 within residue: .R<ILE 2>
> Created a new atom named: HB1 within residue: .R<PHE 3>
> Created a new atom named: HB1 within residue: .R<TYR 5>
> Created a new atom named: HG11 within residue: .R<ILE 6>
> Created a new atom named: HB1 within residue: .R<TRP 7>
> Created a new atom named: HG11 within residue: .R<ILE 11>
> Created a new atom named: HB1 within residue: .R<PHE 12>
> Created a new atom named: HB1 within residue: .R<TYR 14>
> Created a new atom named: HG11 within residue: .R<ILE 15>
> Created a new atom named: HOCA within residue: .R<CVAL 16>
> total atoms in file: 295
> Leap added 12 missing atoms according to residue templates:
> 12 H / lone pairs
> The file contained 12 atoms not in residue templates
> Since added/missing = extra, there is a high probability
> of atoms with 'incorrect' names; you may want to
> use addPdbAtomMap to map these names, or change in file
> > saveamberparm bsheettest bsheettest.top bsheettest.crd
> Checking Unit.
> FATAL: Atom .R<NVAL 1>.A<HNCA 19> does not have a type.
> FATAL: Atom .R<NVAL 1>.A<H 20> does not have a type.
> FATAL: Atom .R<ILE 2>.A<HG11 20> does not have a type.
> FATAL: Atom .R<PHE 3>.A<HB1 21> does not have a type.
> FATAL: Atom .R<TYR 5>.A<HB1 22> does not have a type.
> FATAL: Atom .R<ILE 6>.A<HG11 20> does not have a type.
> FATAL: Atom .R<TRP 7>.A<HB1 25> does not have a type.
> FATAL: Atom .R<ILE 11>.A<HG11 20> does not have a type.
> FATAL: Atom .R<PHE 12>.A<HB1 21> does not have a type.
> FATAL: Atom .R<TYR 14>.A<HB1 22> does not have a type.
> FATAL: Atom .R<ILE 15>.A<HG11 20> does not have a type.
> FATAL: Atom .R<CVAL 16>.A<HOCA 18> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
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