AMBER Archive (2004)

Subject: Re: AMBER: Antechamber compilation: leap error

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Mon Apr 12 2004 - 06:55:11 CDT

Arvind,

        I also met this problem. It is due to atom type in prepi file. You can see that they are all typed DU.

======= 2004-04-12 19:35:58 =======

>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.
>
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= = = = = = = = = = = = = = = = = = = =
                        

　　　　　　　
 
Best regards,
                                 
Ye Mei
ymei_at_itcc.nju.edu.cn
2004-04-12

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