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
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.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery,
> may not
> be read every day, and should not be used for urgent or sensitive
> issues.
>
>
> ----------------------------------------------------------------------
> -
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--------------------------------
Evan Kelly
ekelly9.gmail.com
----------------------------------
Evan Kelly
ebkelly.ualberta.ca
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
- application/octet-stream attachment: VLB.pdb
- application/octet-stream attachment: VLB.prep
Received on Wed Jun 14 2006 - 06:07:13 PDT
