AMBER Archive (2005)

Subject: Re: Re: AMBER:

From: emilia wu (emiliawu_at_dicp.ac.cn)
Date: Tue Apr 05 2005 - 01:43:49 CDT

Dear David,

Thank you for your help. i have checked the input structure,and i can ensure that it is a good one. there are 89 atoms in the molecule,and here i attached the pdb file.


        

======= 2005-04-05 14:06:34 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======

>On Mon, Apr 04, 2005, emilia wu wrote:
>>
>> i am trying to use antechamber to get a prepi file of my molecule,and i
>> input "antechamber -fi gout -fo prepi -i ligand.out -o ligand.prepi -c resp
>> -rn OSC -rf OSC.res -pf y".
>>
>> 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
>>
>> The number of the ESP exceeds the MAXESP(20000),extend the size and
>> reallocate the memory
>
>Is the input structure really a good one (point "(1)" above)? How big is it?
>If you have resp charges, you don't really need bond types, and occasionally
>antehcamber will be unable to assign bond types to a good structure. But
>the messages suggest that it is possible that the molecule is either too big
>for this sort of calculation, or in some way is not a "standard" closed-shell
>organic molecule. If you cannot figure it out, you will probably have to post
>an input structure (either as pdb [preferable] or as gout as you have above.
>
>...good luck...dac
>
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¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡emilia wu
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡emiliawu_at_dicp.ac.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-04-05


  • application/octet-stream attachment: osc.pdb

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