Yong Xu wrote:
>
> Dear Gohlke,
>
> I can't find mm_pbsa_calceneent.pm in $AMBERHOME/src/mm_pbsa.
> there are only mm_pbsa_statistics.pm
> and I can't grep generate_pqr out from all files in that dir.
I was assuming you are using mm_pbsa of Amber8? I don't have an older
version around here, but why don't you try to grep for "No radius found"
- this should occur in mm_pbsa.pl then.
Best regards
Holger
>
> have I installed it correct?
>
> ======= 2004-12-10 09:21:00 您在来信中写道：=======
>
> >Yong Xu wrote:
> >>
> >> Dear Amber-users
> >>
> >> I performed MM-PBSA simulation and encounter some problem.
> >> when I do mm_pbsa.pl mm_pbsa.in >mm_pbsa.log
> >> system give this info:
> >> No radius found for 2412 Zn Zn
> >>
> >> Then I modify "my_delphi.crg" and "my_delphi.siz" by adding Zn parameter, but this information still remain.
> >
> >The error above is unrelated to calculations with delphi, but has to do
> >with the generation of the pqr file for molsurf calculations. You can
> >add an appropriate parameter in the function generate_pqr in the file
> >mm_pbsa_calceneent.pm in $AMBERHOME/src/mm_pbsa to get around.
> >
> >Best regards
> >
> >Holger
> >
> >>
> >> which file should I modify and what should I add?
> >>
> >> Any suggestion would be very appreciated!
> >>
> >> =================
> >> more my_delphi.crg
> >>
> >> !Amber parm94 charges
> >> atom_resnumbc_charge
> >> N MET 1 0.1592
> >> :
> >> :
> >> :
> >> NA+ CIP 1.0000
> >> CL- CIM -1.000
> >> Zn Zn 2.000
> >> C0 C0 2.000
> >> (I added the last two lines ）
> >>
> >> ================
> >> my_delphi.siz：
> >> !my siz based on PARSE
> >> :
> >> :
> >> :
> >> :
> >> Mg 0.99
> >> Zn 1.10
> >> C0 1.71
> >>
> >> (beside Zn2+, there are also Ca2+ ions, so I also added C0 for Ca2+ ions)
> >>
> >>
> >>
> >> Best regard!
> >>
> >> Yong Xu
> >> yxu.mail.sioc.ac.cn
> >> 2004-12-10
> >>
> >> ===========================================================
> >> * 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
> >> ===========================================================
> >>
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber.scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
> >--
> >++++++++++++++++++++++++++++++++++++++++++++++++++
> >Dr. Holger Gohlke
> >
> >J.W. Goethe-Universit鋞
> >Fachbereich Biologie und Informatik
> >Institut f黵 Mikrobiologie
> >Marie-Curie-Str. 9
> >60439 Frankfurt/Main
> >Germany
> >
> >Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29826
> >Email: gohlke.bioinformatik.uni-frankfurt.de
> >URL: http://www.uni-frankfurt.de/~hgohlke
> >++++++++++++++++++++++++++++++++++++++++++++++++++
> >-----------------------------------------------------------------------
> >The AMBER Mail Reflector
> >To post, send mail to amber.scripps.edu
> >To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
> >
> >
> >smg
>
> = = = = = = = = = = = = = = = = = = = =
>
>
> Best regards!
>
> Yong Xu
> yxu.mail.sioc.ac.cn
> 2004-12-10
> ===========================================================
> * 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
> ===========================================================
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
--
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
J.W. Goethe-Universit鋞
Fachbereich Biologie und Informatik
Institut f黵 Mikrobiologie
Marie-Curie-Str. 9
60439 Frankfurt/Main
Germany
Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29826
Email: gohlke.bioinformatik.uni-frankfurt.de
URL: http://www.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
-----------------------------------------------------------------------
The AMBER Mail Reflector
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Received on Fri Dec 10 2004 - 10:53:01 PST
