Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA

From: Yong Xu <yxu.mail.sioc.ac.cn>
Date: Fri, 21 Oct 2005 9:21:33 +0800

Dear Prof. Case

I use following procedure to prepare lig.frcmod and lig.prep file and encounter some problems
===============================================
give a ligand's MOL2 file, lig.mol2
antechamber -i lig.mol2 -fi mol2 -o lig.gjf -fo gcrt
g98 <lig.gjf> lig.out
antechamber -i lig.out -fi gout -o lig.prep -fo prepi -c resp
parmchk -i lig.prep -f prepi -o lig.frcmod
==================================================

(1)
the resultant *.prep file have one line with "nan0x7fffffff". is there something wrong? how to fix it?
when I use this *prep file to do MMPBSA, MMPBSA also give out some result.
please find enclosed no137_1.prep for detail information.

(2) charge in *.prep is not reasonable
I use the same procedure as metioned in question (2) the last column in *.prep file is unreasonable.
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
   4 C1 c3 M 3 2 1 1.540 111.208 180.000 7.110
   5 H4 hx E 4 3 2 1.091 72.182 161.251 -2.552
   6 H5 hx E 4 3 2 1.091 72.180 -78.733 -2.552
   7 H6 hx E 4 3 2 1.091 72.177 41.253 -2.552
   8 N1 n4 M 4 3 2 1.476 180.000 90.000 8.016
for detail info please find enclosed no383_1.prep
I view the pdb file but can't see any problem, so

WHAT is the problem with "antechamber" command ???

thank you for your kindly reply

Yong
        

======= 2005-10-17 08:10:00 David A. Case wrote=======

>On Wed, Oct 12, 2005, Yong Xu wrote:
>>
>> I want to do some MMPBSA work on a series of small molecules composed of F,
>> Cl, Br, or I atoms. but there are no parameter for those elements.
>
>These atoms have not been parameterized in the Amber scheme (as far as I
>know), but the "Bondi" radii should give good starting points:
>
> A. Bondi
> J. Chem. Phys.
> 64
> 441
> 1964
>
>Maybe some list-members who have done large scale calculations can pitch in
>with ideas. Note that the only thing "missing" are parameters for the surface
>area part (please let me know if I am wrong here), and I don't think that
>small uncertainties in the parameters for halogens would lead to much overall
>uncertainty in the final results: getting good charges (and therefore good C-X
>bond dipoles) is probably much more important.
>
>....dac
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= = = = = = = = = = = = = = = = = = = =
                        

Best regards!
                                 
        Yong Xu
        yxu.mail.sioc.ac.cn
          2005-10-21
===========================================================
* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Science
           
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
        
* Email: yxu.mail.sioc.ac.cn
* yxuemail.sina.com
===========================================================
      



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Received on Fri Oct 21 2005 - 02:53:03 PDT
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