Hi all,
I'm getting the following error when i try to compile antechamber
make test.antechamber
cd antechamber/tp; ./Run.tp
Running: /usr/local/amber7/exe/mopac.sh ANTECHAMBER_MUL.MOP
ANTECHAMBER_MUL.OUT
Running: /usr/local/amber7/exe/bcctype -i ANTECHAMBER_BCC_PRE.AC -o
ANTECHAMBER_BCC_TYPE.AC -f ac -p
/usr/local/amber7/dat/antechamber/BCCTYPE.DEF -j both
Running: /usr/local/amber7/exe/bcc -i ANTECHAMBER_BCC_TYPE.AC -o
ANTECHAMBER_BCC.AC -p /usr/local/amber7/dat/BCCPARM.DAT
Running: /usr/local/amber7/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o
ANTECHAMBER_PREP.AC -p gaff
Running: /usr/local/amber7/exe/prepgen -i ANTECHAMBER_PREP.AC -f int -o
tp.prepin -rn "TP " -rf molecule.res
.../../../exe/parmchk -i tp.prepin -f prepi -o frcmod
.../../../exe/tleap -s -f leap.in > leap.out
diffing tp.prepin.save with tp.prepin
possible FAILURE: check tp.prepin.dif
==============================================================
diffing frcmod.save with frcmod
possible FAILURE: check frcmod.dif
==============================================================
diffing prmtop.save with prmtop
grep: prmtop: No such file or directory
possible FAILURE: check prmtop.dif
==============================================================
cd antechamber/ash; ./Run.ash
Running: /usr/local/amber7/exe/mopac.sh ANTECHAMBER_MUL.MOP
ANTECHAMBER_MUL.OUT
.../../../exe/parmchk -i ash.prepin -f prepi -o frcmod
.../../../exe/tleap -s -f leap.in > leap.out
Program error
make: *** [test.antechamber] Error 1
This is the leap.log file:
log started: Wed Apr 14 23:19:28 2004
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" }
>> { "cd" "C" "sp2" }
>> { "n" "N" "sp2" }
>> { "n1" "N" "sp2" }
>> { "n2" "N" "sp2" }
>> { "n3" "N" "sp3" }
>> { "n4" "N" "sp3" }
>> { "na" "N" "sp2" }
>> { "nb" "N" "sp2" }
>> { "nd" "N" "sp2" }
>> { "nh" "N" "sp2" }
>> { "no" "N" "sp2" }
>> { "s2" "S" "sp2" }
>> { "s3" "S" "sp3" }
>> { "s4" "S" "sp3" }
>> { "s6" "S" "sp3" }
>> { "sh" "S" "sp3" }
>> { "ss" "S" "sp3" }
>> { "p2" "P" "sp2" }
>> { "p3" "P" "sp3" }
>> { "p4" "P" "sp3" }
>> { "p5" "P" "sp3" }
>> { "pd" "P" "sp3" }
>> { "f" "F" "sp3" }
>> { "cl" "Cl" "sp3" }
>> { "br" "Br" "sp3" }
>> { "i" "I" "sp3" }
>> { "lp" "" "sp3" }
>> }
>> #
>> # Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading parameters: /usr/local/amber7/dat/leap/parm/gaff.dat
(UNKNOWN ATOM TYPE: lp)
>
> mods = loadamberparams frcmod
Loading parameters: ./frcmod
Reading force field mod type file (frcmod)
(UNKNOWN ATOM TYPE: DU)
> loadamberprep ash.prepin
Loading Prep file: ./ash.prepin
** This is a remark line: 'IMPROPER' atom CH3 not found
** This is a remark line: 'IMPROPER' atom O not found
** This is a remark line: 'IMPROPER' atom C not found
** This is a remark line: 'IMPROPER' atom N not found
** This is a remark line: 'IMPROPER' atom CA not found
** This is a remark line: 'IMPROPER' atom O not found
** This is a remark line: 'IMPROPER' atom C not found
** This is a remark line: 'IMPROPER' atom N not found
** This is a remark line: 'IMPROPER' atom CB not found
** This is a remark line: 'IMPROPER' atom OD2 not found
** This is a remark line: 'IMPROPER' atom CG not found
** This is a remark line: 'IMPROPER' atom OD1 not found
Loaded UNIT: ACE
> saveamberparm ACE prmtop prmcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
total 0 improper torsions applied
0 improper torsions in old prep form
Building H-Bond parameters.
Marking per-residue atom chain types.
ACE: no atoms
(no restraints)
It seems there are a lot of improper atom types in the ash.prepin file.
This is the ash.prepin file, in case, its relevant:
0 0 2
This is a remark line
molecule.res
ACE XYZ 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 CH3 DU M 3 2 1 1.540 111.208 180.000 -0.172
5 HH31 DU E 4 3 2 1.090 90.000 0.000 0.080
6 HH32 DU E 4 3 2 1.090 61.873 -112.244 0.067
7 HH33 DU E 4 3 2 1.090 61.873 112.244 0.062
8 C DU M 4 3 2 1.530 158.887 180.000 0.661
9 O DU E 8 4 3 1.230 120.489 180.000 -0.613
10 N DU M 8 4 3 1.335 116.614 0.000 -0.575
11 H DU E 10 8 4 1.009 119.984 0.000 0.338
12 CA DU M 10 8 4 1.449 121.890 180.000 0.057
13 HA DU E 12 10 8 1.090 109.542 -60.011 0.097
14 C DU B 12 10 8 1.521 111.109 -180.000 0.641
15 O DU E 14 12 10 1.229 120.511 0.000 -0.621
16 N DU B 14 12 10 1.335 116.648 180.000 -0.560
17 H DU E 16 14 12 1.010 119.959 0.000 0.338
18 CH3 DU 3 16 14 12 1.449 121.928 -180.000 0.076
19 HH31 DU E 18 16 14 1.090 109.516 0.000 0.076
20 HH32 DU E 18 16 14 1.090 109.502 120.008 0.034
21 HH33 DU E 18 16 14 1.090 109.502 -120.008 0.033
22 CB DU M 12 10 8 1.525 111.108 60.004 -0.160
23 HB2 DU E 22 12 10 1.090 109.509 -60.053 0.118
24 HB3 DU E 22 12 10 1.090 109.509 59.964 0.097
25 CG DU M 22 12 10 1.527 109.499 179.988 0.648
26 OD2 DU S 25 22 12 1.260 117.182 -89.966 -0.599
27 HD2 DU E 26 25 22 0.961 109.454 179.969 0.448
28 OD1 DU M 25 22 12 1.260 117.179 89.958 -0.572
LOOP
IMPROPER
CH3 O C N
CA O C N
CB OD2 CG OD1
DONE
STOP
Can somebody tell me what's happening? Is it the problem with the
ash.prepin file? Or is it something else? I'm using amber7, redhat9.
Thanx in advance.
Regards,
Arvind.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Apr 12 2004 - 12:53:00 PDT
