In addition to what reported in previous mail below, this morning I
have renumbered from #4 to #1 residue PHA in starting pha.NH3.pdb.
Then, pha.mol2 from antechamber (open correctly in VMD) and pha.frcmod
from parmchk.
From these mol2 and frcmod files, xleap now produced pha.prmtop and
pha.inpcrd (no crash, no hanging).
Chimera movie is unable to load these prmtop/inpcrd: error, index out
of range. VMD loads them, however (as with the older compilation of
ambertools.1.2, only 1-5 bugfixed) the molecule is highly distorted as
to NH2 (of CONH2) and the phenyl ring.
There was no error signal, nor any major warning. I don't see anything
wrong in leap.log:
*********************
log started: Mon Oct 4 10:33:51 2010
Log file: ./leap.log
> #
> # ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
> #
> # load atom type hybridizations
> #
> addAtomTypes {
> { "H" "H" "sp3" }
> { "HO" "H" "sp3" }
> { "HS" "H" "sp3" }
> { "H1" "H" "sp3" }
> { "H2" "H" "sp3" }
> { "H3" "H" "sp3" }
> { "H4" "H" "sp3" }
> { "H5" "H" "sp3" }
> { "HW" "H" "sp3" }
> { "HC" "H" "sp3" }
> { "HA" "H" "sp3" }
> { "HP" "H" "sp3" }
> { "OH" "O" "sp3" }
> { "OS" "O" "sp3" }
> { "O" "O" "sp2" }
> { "O2" "O" "sp2" }
> { "OW" "O" "sp3" }
> { "CT" "C" "sp3" }
> { "CH" "C" "sp3" }
> { "C2" "C" "sp3" }
> { "C3" "C" "sp3" }
> { "C" "C" "sp2" }
> { "C*" "C" "sp2" }
> { "CA" "C" "sp2" }
> { "CB" "C" "sp2" }
> { "CC" "C" "sp2" }
> { "CN" "C" "sp2" }
> { "CM" "C" "sp2" }
> { "CK" "C" "sp2" }
> { "CQ" "C" "sp2" }
> { "CD" "C" "sp2" }
> { "CE" "C" "sp2" }
> { "CF" "C" "sp2" }
> { "CG" "C" "sp2" }
> { "CP" "C" "sp2" }
> { "CI" "C" "sp2" }
> { "CJ" "C" "sp2" }
> { "CW" "C" "sp2" }
> { "CV" "C" "sp2" }
> { "CR" "C" "sp2" }
> { "CA" "C" "sp2" }
> { "CY" "C" "sp2" }
> { "C0" "C" "sp2" }
> { "MG" "Mg" "sp3" }
> { "N" "N" "sp2" }
> { "NA" "N" "sp2" }
> { "N2" "N" "sp2" }
> { "N*" "N" "sp2" }
> { "NP" "N" "sp2" }
> { "NQ" "N" "sp2" }
> { "NB" "N" "sp2" }
> { "NC" "N" "sp2" }
> { "NT" "N" "sp3" }
> { "N3" "N" "sp3" }
> { "S" "S" "sp3" }
> { "SH" "S" "sp3" }
> { "P" "P" "sp3" }
> { "LP" "" "sp3" }
> { "F" "F" "sp3" }
> { "CL" "Cl" "sp3" }
> { "BR" "Br" "sp3" }
> { "I" "I" "sp3" }
> { "FE" "Fe" "sp3" }
> { "EP" "" "sp3" }
> # glycam
> { "OG" "O" "sp3" }
> { "OL" "O" "sp3" }
> { "AC" "C" "sp3" }
> { "EC" "C" "sp3" }
> }
> #
> # Load the main parameter set.
> #
> parm99 = loadamberparams parm99.dat
Loading parameters: /usr/local/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
(UNKNOWN ATOM TYPE: HZ)
(UNKNOWN ATOM TYPE: NY)
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: Li)
(UNKNOWN ATOM TYPE: IP)
(UNKNOWN ATOM TYPE: K)
(UNKNOWN ATOM TYPE: Rb)
(UNKNOWN ATOM TYPE: Cs)
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: IB)
(UNKNOWN ATOM TYPE: LP)
> frcmod99SB = loadamberparams frcmod.ff99SB
Loading parameters: /usr/local/amber10/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
> #
> # Load DNA/RNA libraries
> #
> loadOff all_nucleic94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_nucleic94.lib
Loading: DA
Loading: DA3
Loading: DA5
Loading: DAN
Loading: DC
Loading: DC3
Loading: DC5
Loading: DCN
Loading: DG
Loading: DG3
Loading: DG5
Loading: DGN
Loading: DT
Loading: DT3
Loading: DT5
Loading: DTN
Loading: RA
Loading: RA3
Loading: RA5
Loading: RAN
Loading: RC
Loading: RC3
Loading: RC5
Loading: RCN
Loading: RG
Loading: RG3
Loading: RG5
Loading: RGN
Loading: RU
Loading: RU3
Loading: RU5
Loading: RUN
> #
> # Load main chain and terminating
> # amino acid libraries (i.e. ff94 libs)
> #
> loadOff all_amino94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_amino94.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
> loadOff all_aminoct94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminoct94.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
> loadOff all_aminont94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminont94.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
> #
> # Load water and ions
> #
> loadOff ions94.lib
Loading library: /usr/local/amber10/dat/leap/lib/ions94.lib
Loading: CIO
Loading: Cl-
Loading: Cs+
Loading: IB
Loading: K+
Loading: Li+
Loading: MG2
Loading: Na+
Loading: Rb+
> loadOff solvents.lib
Loading library: /usr/local/amber10/dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
> HOH = TP3
> WAT = TP3
>
> #
> # Define the PDB name map for the amino acids and DNA.
> #
> addPdbResMap {
> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
> { 0 "HID" "NHID" } { 1 "HID" "CHID" }
> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
> { 0 "MET" "NMET" } { 1 "MET" "CMET" }
> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
> { 0 "SER" "NSER" } { 1 "SER" "CSER" }
> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
> { 0 "G" "DG5" } { 1 "G" "DG3" } { "G" "DG" } { "GN" "DGN" }
> { 0 "A" "DA5" } { 1 "A" "DA3" } { "A" "DA" } { "AN" "DAN" }
> { 0 "C" "DC5" } { 1 "C" "DC3" } { "C" "DC" } { "CN" "DCN" }
> { 0 "T" "DT5" } { 1 "T" "DT3" } { "T" "DT" } { "TN" "DTN" }
> { 0 "C5" "DC5" }
> { 0 "G5" "DG5" }
> { 0 "A5" "DA5" }
> { 0 "T5" "DT5" }
> { 1 "C3" "DC3" }
> { 1 "G3" "DG3" }
> { 1 "A3" "DA3" }
> { 1 "T3" "DT3" }
>
> }
>
> addPdbAtomMap {
> { "O5*" "O5'" }
> { "C5*" "C5'" }
> { "C4*" "C4'" }
> { "O4*" "O4'" }
> { "C3*" "C3'" }
> { "O3*" "O3'" }
> { "C2*" "C2'" }
> { "C1*" "C1'" }
> { "C5M" "C7" }
> { "H1*" "H1'" }
> { "H2*1" "H2'1" }
> { "H2*2" "H2'2" }
> { "H3*" "H3'" }
> { "H4*" "H4'" }
> { "H5*1" "H5'1" }
> { "H5*2" "H5'2" }
> # old ff atom names -> new
> { "O1'" "O4'" }
> { "OA" "O1P" }
> { "OB" "O2P" }
> }
>
>
> #
> # assumed that most often proteins use HIE
> #
> NHIS = NHIE
> HIS = HIE
> CHIS = CHIE
> source leaprc.gaff
----- Source: /usr/local/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber10/dat/leap/cmd/leaprc.gaff done
>> logFile leap.log
log started: Mon Oct 4 10:34:03 2010
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> # This file is mostly for use with Antechamber
>> #
>> # load atom type hybridizations
>> #
>> addAtomTypes {
>> { "h1" "H" "sp3" }
>> { "h2" "H" "sp3" }
>> { "h3" "H" "sp3" }
>> { "h4" "H" "sp3" }
>> { "h5" "H" "sp3" }
>> { "ha" "H" "sp3" }
>> { "hc" "H" "sp3" }
>> { "hn" "H" "sp3" }
>> { "ho" "H" "sp3" }
>> { "hp" "H" "sp3" }
>> { "hs" "H" "sp3" }
>> { "hw" "H" "sp3" }
>> { "hx" "H" "sp3" }
>> { "o" "O" "sp2" }
>> { "o2" "O" "sp2" }
>> { "oh" "O" "sp3" }
>> { "os" "O" "sp3" }
>> { "ow" "O" "sp3" }
>> { "c" "C" "sp2" }
>> { "c1" "C" "sp2" }
>> { "c2" "C" "sp2" }
>> { "c3" "C" "sp3" }
>> { "ca" "C" "sp2" }
>> { "cc" "C" "sp2" }
>> { "cd" "C" "sp2" }
>> { "ce" "C" "sp2" }
>> { "cf" "C" "sp2" }
>> { "cg" "C" "sp2" }
>> { "ch" "C" "sp2" }
>> { "cp" "C" "sp2" }
>> { "cq" "C" "sp2" }
>> { "cu" "C" "sp2" }
>> { "cv" "C" "sp2" }
>> { "cx" "C" "sp2" }
>> { "cy" "C" "sp2" }
>> { "n" "N" "sp2" }
>> { "n1" "N" "sp2" }
>> { "n2" "N" "sp2" }
>> { "n3" "N" "sp3" }
>> { "n4" "N" "sp3" }
>> { "na" "N" "sp2" }
>> { "nb" "N" "sp2" }
>> { "nc" "N" "sp2" }
>> { "nd" "N" "sp2" }
>> { "ne" "N" "sp2" }
>> { "nf" "N" "sp2" }
>> { "nh" "N" "sp2" }
>> { "no" "N" "sp2" }
>> { "s" "S" "sp2" }
>> { "s2" "S" "sp2" }
>> { "s3" "S" "sp3" }
>> { "s4" "S" "sp3" }
>> { "s6" "S" "sp3" }
>> { "sh" "S" "sp3" }
>> { "ss" "S" "sp3" }
>> { "sx" "S" "sp3" }
>> { "sy" "S" "sp3" }
>> { "p2" "P" "sp2" }
>> { "p3" "P" "sp3" }
>> { "p4" "P" "sp3" }
>> { "p5" "P" "sp3" }
>> { "pb" "P" "sp3" }
>> { "pd" "P" "sp3" }
>> { "px" "P" "sp3" }
>> { "py" "P" "sp3" }
>> { "f" "F" "sp3" }
>> { "cl" "Cl" "sp3" }
>> { "br" "Br" "sp3" }
>> { "i" "I" "sp3" }
>> }
>> #
>> # Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading parameters: /usr/local/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
>
> x = loadmol2 pha.mol2
Loading Mol2 file: ./pha.mol2
Reading MOLECULE named PHA
> check x
Checking 'x'....
WARNING: The unperturbed charge of the unit: 1.000100 is not zero.
Checking parameters for unit 'x'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
> loadamberparams pha.frcmod
Loading parameters: ./pha.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> saveoff x pha.lib
Creating pha.lib
Saving x.
Building topology.
Building atom parameters.
> saveamberparm x pha.prmtop pha.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 1.000100 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 8 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
PHA 1
)
(no restraints)
*****************************************
Thanks for your kind attention
francesco pietra
On Sun, Oct 3, 2010 at 11:44 PM, Francesco Pietra <chiendarret.gmail.com> wrote:
> On Fri, Oct 1, 2010 at 1:35 PM, case <case.biomaps.rutgers.edu> wrote:
>> On Fri, Oct 01, 2010, Francesco Pietra wrote:
>>
>>> At a fresh check this morning, the residue number 4 in the for-last
>>> column of the mol2 file was the problem. Replacing 4 with 1, the mol2
>>> file was loaded by xleap. Now I'll see if I can build prmtop/inpcrd
>>> for the peptide.
>>
>> This sounds like bugfix 10 to version 1.2 has not been applied. If that is
>> the case, it's probably worth upgrading to the latest version.
>
> Recompiled ambertools.1.2/gcc for current bugfix.all and amber.10/gfortran.
>
> Reprepared pha.mol2 with new antechamber and pha.frcmod with new parmchk.
>
> $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leapcrd.ff99SB
>
> source leaprc.gaff
>
> x = loadmol2 pha.mol2 (where pha.mol2 has PHA residue numbered 4 like
> in the mol2 file that I showed before) (same as previously, apart very
> slight differences in the charge values)
>
> xleap crashed. Such a crash was an alternative to hanging, i.e. one of
> the two occurred, even on previous attempts with older compilation of
> ambertools.1.2.
>
> As sustiva.mol2 (tutorial b4) is treated correctly by xleap, there
> must be something wrong in pha.mol2 . Such oddness is not detected by
> VMD. It also opens correctly, although currently Chimera treats by
> pseudobonds the aromatic rings in mol2 files.
>
> As to now I have no better ideas.
>
> Thanks
> francesco
>
>
>>
>> ....dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Mon Oct 04 2010 - 02:00:03 PDT
