AMBER Archive (2005)

Subject: Re: RE: Re: AMBER:

From: emilia wu (emiliawu_at_dicp.ac.cn)
Date: Tue Apr 05 2005 - 07:25:42 CDT

Dear David ,

thank you for your reply! Everything is working fine now.
thanks again !

emilia

        

======= 2005-04-05 15:13:56 ÄúÔÚÀ´ÐÅÖÐдµÀ£º=======

>Dear Emily -
>
>I was able to take your OSC.pdb file and move it through antechamber and leap (Amber8 versions) without any problems (default programs with no special compilation).
>
>antechamber -fi pdb -i osc.pdb -fo prepi -o osc.prepin -c bcc -rn OSC
>
>Note I used the bcc charge option. In my very limited experience I've had little success with esp. It has never extracted esp charges from a Gaussian output (even when that run used the pop=mk keyword). You could type your own esp values in the prepin file if you wanted, or do this from xleap. Then in tleap:
>
>>source leaprc.gaff
>>loadamberprepin osc.prepin
>>check osc (finds a few missing parameters, but that is not unexpected)
>>saveoff OSC osc.off
>
>I've attached the resulting osc.prepin and osc.off files.
>
>Not as good as TLC from DAC, but just wanted to lend a hand.
>
>Cheers,
>Dave
>
>
>
>-----Original Message-----
>From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of emilia wu
>Sent: Tuesday, April 05, 2005 6:44 AM
>To: amber_at_scripps.edu
>Subject: Re: Re: AMBER:
>
>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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>
>= = = = = = = = = = = = = = = = = = = =
>
>
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÖÂ
>Àñ£¡
>
>
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡emilia wu
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡emiliawu_at_dicp.ac.cn
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-04-05

= = = = = = = = = = = = = = = = = = = =
        
                                 
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡emilia wu
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡emiliawu_at_dicp.ac.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-04-05

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