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--- ----- Original Message ----- From: "FyD" <fyd.u-picardie.fr> To: "Xin Hu" <hux.mail.rockefeller.edu> Sent: Tuesday, June 01, 2004 2:08 PM Subject: Re: question > Hi, > > > I am very interested in RED. It is a powerful tool. One question is I > > feel it is unconvenient to define the atom name in PDB files. Actually I > > always get confused when I try to modify the atom name mannually. > > Uauslly I get the PDB file (or Mol2 file) from Sybyl . Is there any > > convenient way to convert the pdb or mol2 file to the right format to > > input for RED? > > I know such part might not be seen as very convenient, but it is really improved > in the R.E.D. version 2.0 were the PDB names allows to generate also > non-standard RESP inputs, using or not the "T" character... > However, I think that the fact that the user has to 'think' about the RESP > inputs is not that a bad think, after all... The proof: See below because I > think you did mistakes to prepare the PDB atom names for RESP input > generation... > > For the automatic convertion of PDB/mol2 files, you can use babel. > babel -ipdb toto.pdb -omol2 toto.mol2 > or > babel -imol2 toto.mol2 -opdb toto.pdb > > But you still have to modify the PDB atom names manually... > > I do not really agree with the way you equivalenced your benzyl.pdb file: I > would use instead: > ATOM 1 CT1 BEN 1 2.506 0.000 0.000 > ATOM 2 H1 BEN 1 2.872 0.268 -1.002 > ATOM 3 H1 BEN 1 2.872 0.733 0.733 > ATOM 4 H1 BEN 1 2.872 -1.002 0.268 > ATOM 5 C2 BEN 1 0.981 0.000 0.000 > ATOM 6 C3 BEN 1 0.281 -1.211 0.000 ortho > ATOM 7 H3 BEN 1 0.824 -2.150 0.000 > ATOM 8 C4 BEN 1 -1.117 -1.211 0.000 meta > ATOM 9 H4 BEN 1 -1.659 -2.150 0.000 > ATOM 10 C5 BEN 1 -1.816 0.000 0.000 para > ATOM 11 H5 BEN 1 -2.900 0.000 0.000 > ATOM 12 C4 BEN 1 -1.117 1.211 0.000 meta > ATOM 13 H4 BEN 1 -1.659 2.150 0.000 > ATOM 14 C3 BEN 1 0.281 1.211 0.000 ortho > ATOM 15 H3 BEN 1 0.824 2.150 0.000 > > The 'ortho' atoms to Methyl group should be equivalenced in the 1st RESP input. > Same for the 'meta'... > > > Attached is a very simple compounds benzyl group. I defined the methyl > > carbone as CT1 (the three H1 H1 H1) and the six aromatic carbone as C2 > > C3 C4 C5 C6 C7 and the six equentlent hydrogen as H8. However, the > > program doesn't work on it. No coordinations were wrote into the gamess > > input file .inp. > > Can you have a try? > > See http://www.u-picardie.fr/labo/lbpd/RED/bugs > ------------- 2nd bug report --------------------- > > This bug has been corrected in the R.E.D. version 2.0 > > > Another question, I try to use XRED.pl. Both RED.pl and XRED.pl in the > > working directory, but when I "start" the XRED, it shows no RED was > > found. How to fix the problem? > > What is your O.S., machine, and 'wish' version? > To use X RED you need 'wish version 8.3.5' (or newer) and to set XRED = "on" in > RED.pl line 1234; see RED.pdf manual page 5 and 8. > > > Thank you for your help. > > You are wellcome. > Please ask your future questions in the AMBER mailing list. > > Kind regards, Francois > > F.-Y. Dupradeau > -- > The Scripps Research Institute, San Diego, CA > Faculte de Pharmacie, UPJV, Amiens, France > -- > http://www.u-picardie.fr/labo/lbpd/fyd.htm > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Wed Jun 02 2004 - 00:53:00 PDT