AMBER Archive (2006)

Subject: Re: AMBER: parmchk error

From: Evan Kelly (ebkelly_at_ualberta.ca)
Date: Tue Jun 13 2006 - 00:42:16 CDT

Hi,

As per the conversation below, here are the inputted (to
antechamber) .pdb file and the resulting prepi file. I call parmchk as:

parmchk -i VLB.prep -o VLB.frcmod -f prepi


  • application/octet-stream attachment: VLB.pdb

  • application/octet-stream attachment: VLB.prep

Thanks for the help!

On 12-Jun-06, at 9:31 AM, Ross Walker wrote:

> Hi Evan,
>
>> I have used antechamber to set up a prepi file for an organic ligand
>> I want to study. The ligand has 117 atoms. There are two missing
>> parameters, and so I tried to run parmchk to create an frcmod file.
>> However, I am met with many repetitions of the following:
>>
>> Info: the atom number exceeds the MAXATOM, reallocate memory
>> automatically
>>
>> which doesn't cause much concern, but then the following
>> error occurs
>> many times:
>>
>> Unrecognized atomic name , exit
>>
>> which is followed by a segmentation fault. Can anybody suggest what
>> the problem is?
>
> I suspect your input file has the incorrect format and/or this has
> lead to
> problems in the prep file. Can you post the input file and the prep
> file
> that you got (or send them to me privately). This will make it
> easier to see
> what is going wrong.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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--------------------------------
Evan Kelly
ekelly9_at_gmail.com

----------------------------------
Evan Kelly
ebkelly_at_ualberta.ca

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