AMBER Archive (2005)

Subject: Re: RE: RE: AMBER: Antechamber RESP failed for large organic molecule

From: junwang (junwang_at_unlserve.unl.edu)
Date: Wed Jun 01 2005 - 16:18:05 CDT

Dear Dr. Junmei Wang:

Yes, I have ANTECHAMBER_RESP1.IN and ANTECHAMBER_RESP2.IN produced in my directory and they are looking fine as far as I know. I put them as attachments in this e-mail for you to check. I am sure resp program can be run properly because I successfully use it to produce resp charges for my small orginic cation(10 atoms). But it failed when I tried to get resp charges for my large organic molecule(132 atoms).
Right now I've decided to directly use esp charge from Gaussian instead. I think this could be fine enough in my case of studying ion transport inside some kind of organic ion channel.

Best regards,
Sincerely,
Jun WANG

Department of Chemistry
University of Nebraska-Lincoln
536 Hamilton Hall
Lincoln, NE 68588-0304
U.S.A.
E-mail:junwang_at_unlserve.unl.edu
       junwang_at_bigred.unl.edu

======= 2005-06-01 11:54:00 in your letter you mentioned that£º=======

>Hello Jun,
>I can't sure which step cause the problem. Do you have "ANTECHAMBER_RESP1.IN" and " ANTECHAMBER_RESP2.IN" in the directory? Those two files are resp input files. If they are fine, you may check if resp program can be run properly. By the way, how many atoms does your molecule have?
>
>Best
>
>Junmei
>
>
>
>
>==================================================
>Dr. Junmei Wang
>Chemistry & Biophysics
>Encysive Pharmaceuticals Inc.
>7000 Fannin, Houston TX 77030
>Tel: 713-578-6649
>Email: jwang_at_encysive.com
>http://amber.scripps.edu/antechamber/antechamber.html
>==================================================
>
>
>-----Original Message-----
>From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of junwang
>Sent: Tuesday, May 31, 2005 11:59 AM
>To: amber_at_scripps.edu
>Subject: Re: RE: AMBER: Antechamber RESP failed for large organic molecule
>
>
>Dear Dr. Junmei Wang:
>
>But I did not get the expected MER.prepin file because the charge file QOUT was not produced.
>
>
>Best regards,
>Sincerely,
>Jun WANG
>
>Department of Chemistry
>University of Nebraska-Lincoln
>536 Hamilton Hall
>Lincoln, NE 68588-0304
>U.S.A.
>E-mail:junwang_at_unlserve.unl.edu
> junwang_at_bigred.unl.edu
>
>======= 2005-05-31 09:37:00 in your letter you mentioned that$B!'(J=======
>
>>The respgen program automatically expends the sizes of arrays and the
>>result is OK, just ignore the warning message.
>>
>>All the best
>>Junmei
>>
>>==================================================
>>Dr. Junmei Wang
>>Chemistry & Biophysics
>>Encysive Pharmaceuticals Inc.
>>7000 Fannin, Houston TX 77030
>>Tel: 713-578-6649
>>Email: jwang_at_encysive.com
>>http://amber.scripps.edu/antechamber/antechamber.html
>>==================================================
>>
>>
>>Dear AMBER developers and users:
>>
>>I succeeded in creating user-defined residule template .prepin file by
>>antechamber with resp charging method for a small organic molecule(10
>>atoms). But when I fed the Gaussian output file(.log) for a large
>>molecule(132 atoms) to antechamber with the command "antechamber -i
>>MER.log -fi gout -o MER.prepin -fo prepi -c resp -s 2", the resp charge
>>fitting process failed with the following report: the number of the
>>path atoms exceeds(MAXPATHATOMNUM=10000) for atom[0],extend the size
>>and reallocate the memory the number of the path atoms
>>exceeds(MAXPATHATOMNUM=10000) for atom[1],extend the size and
>>reallocate the memory .. .. lib-4001 : UNRECOVERABLE library error ..
>>.. Can not open charge file QOUT, exit
>>
>>But after checking MER.log file by hand, everything looks fine.
>>Mulliken charges and ESP charges have been assigned to each atom.
>>
>>Does this mean I need to modify parameter MAXPATHATOMNUM in some file?
>>
>>
>>Best regards,
>>Sincerely,
>>Jun WANG
>>
>>Department of Chemistry
>>University of Nebraska-Lincoln
>>536 Hamilton Hall
>>Lincoln, NE 68588-0304
>>U.S.A.
>>E-mail:junwang_at_unlserve.unl.edu
>> junwang_at_bigred.unl.edu
>>
>>
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