AMBER Archive (2005)

Subject: RE: Re: AMBER:

From: Wells, David H (d.h.wells_at_imperial.ac.uk)
Date: Tue Apr 05 2005 - 02:13:56 CDT

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 您在来信中写道：=======

>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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= = = = = = = = = = = = = = = = = = = =
                        

　　　　　　　　致
礼！
 
                                 
　　　　　　　　emilia wu
　　　　　　　　emiliawu_at_dicp.ac.cn
　　　　　　　　　　2005-04-05



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