AMBER Archive (2008)

Subject: Re: AMBER: problems of antechamber

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Tue Jan 22 2008 - 08:45:26 CST

Hi Junmei:
    Thank you very much for helping me to solve the problem of
antechamber, The problem I encountered was due to the old version of
antechamber. Afterward I downloaded the latest version of antechamber
and the prepi file was successfully done. But now a new problem
appeared and I cannot solve it by myself.
     The minimization of my system cannot be successfully done and the
wrong information is as follows and I send you all the files needed
for calculation in the attached tar file.
---------
    NSTEP ENERGY RMS GMAX NAME NUMBER
    2750 -2.5808E+07 1.1368E+11 4.8684E+12 O14 28

  BOND = 339.6183 ANGLE = 194.3831 DIHED =
42.5814
  VDWAALS = 614.2881 EEL = -7420.2476 HBOND =
0.0000
  1-4 VDW = 3.5400 1-4 EEL = ************* RESTRAINT =
0.0000

    NSTEP ENERGY RMS GMAX NAME NUMBER
    2800 -1.4185E+08 3.4357E+12 1.4714E+14 H13 30

  BOND = 339.6184 ANGLE = 194.3832 DIHED =
42.5814
  VDWAALS = 614.2881 EEL = -7420.2476 HBOND =
0.0000
  1-4 VDW = 3.5400 1-4 EEL = ************* RESTRAINT =
0.0000

    NSTEP ENERGY RMS GMAX NAME NUMBER
    2850 -3.5276E+07 2.1242E+11 9.0971E+12 H13 30

  BOND = 339.6185 ANGLE = 194.3833 DIHED =
42.5814
  VDWAALS = 614.2881 EEL = -7420.2475 HBOND =
0.0000
  1-4 VDW = 3.5400 1-4 EEL = ************* RESTRAINT =
0.0000

    NSTEP ENERGY RMS GMAX NAME NUMBER
    2900 -1.2849E+08 2.8189E+12 1.2072E+14 O14 28

  BOND = 339.6183 ANGLE = 194.3832 DIHED =
42.5814
  VDWAALS = 614.2881 EEL = -7420.2476 HBOND =
0.0000
  1-4 VDW = 3.5400 1-4 EEL = ************* RESTRAINT =
0.0000

    NSTEP ENERGY RMS GMAX NAME NUMBER
    2950 -3.1666E+07 1.7116E+11 7.3302E+12 H13 30

  BOND = 339.6185 ANGLE = 194.3833 DIHED =
42.5814
  VDWAALS = 614.2881 EEL = -7420.2475 HBOND =
0.0000
  1-4 VDW = 3.5400 1-4 EEL = ************* RESTRAINT =
0.0000

    NSTEP ENERGY RMS GMAX NAME NUMBER
    3000 -6.7296E+07 7.7319E+11 3.3113E+13 H13 30

  BOND = 339.6184 ANGLE = 194.3833 DIHED =
42.5814
  VDWAALS = 614.2881 EEL = -7420.2476 HBOND =
0.0000
  1-4 VDW = 3.5400 1-4 EEL = ************* RESTRAINT =
0.0000

      .... RESTARTED DUE TO LINMIN FAILURE ...
----------------------
Thanks you very much for your reply.

With best regards.
Xi Chen

On Fri, 18 Jan 2008 00:24:52 -0500, Junmei Wang <junmwang_at_gmail.com> wrote:

> Hi,
> For your molecule, I have no problem to generate the correct prepi file,
> although it is highly charged molecule. Which version of antechamber did
> you use? I also attached the prepi file with this email
>
> Best
>
> Junmei
>
>
> On Jan 17, 2008 8:15 PM, liu junjun <ljjlp03_at_gmail.com> wrote:
>
>> Dear Amber:
>> Thanks for your program of antechamber.
>> I have encountered a question the day before yesterday when I
>> used the antechamber to prepare the prepi file of a small molecular
>> which is high-charged with -6 electrons. I assigned the am1-bcc
>> charges to the molecular and the error information is that:
>>
>> Cannot successfully assign bond type for this molecule, please :
>> (1) double check the structure (the connectivity) and/or
>> (2) adjust atom valence penalty parameters in APS.DAT, and/or
>> (3) increase MAXVASTATE in define.h and recompile bondtype.C
>>
>> However the prepi file can be made by antechamber. But when I do
>> the molecular dynamic simmulation, the small molecular cannot be
>> minimized normally, two atoms bumped with each other. The item of 1-4
>> EEL = ************
>> Now I give you the mol2 file of this molecular for your check.
>> With best regards.
>>
>> Xi Chen
>>
>> College of Chemistry, Huazhong Normal University
>> Wuhan, 430079, China
>> 

-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China

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