Hi Urszula,
It is a simple question, so I can answer ;0
The optimization output is generally the file obtained from a QM program (in
red GAUSSIAN, GAMESS, etc.). Provide this file is only option in RED. If you
have not any QM out file(s), you can use only the p2n (Mol_red1-out.p2n
renamed Mol_red1.p2n) with the additional info (i.e. INTER-MCC, INTRA-MMC,
etc.).
HTH
Stefane
-----Message d'origine-----
De : Urszula Uciechowska [mailto:urszula.uchiechowska.chem.umu.se]
Envoyé : jeudi 17 novembre 2011 14:20
À : AMBER Mailing List
Objet : [AMBER] question to R.E.D server
Dear Francois,
I would like to submit a job to R.E.D sever to get charges and generate FF
library for my molecular fragment PYA (p2n file is attached)
during the submission stages (R.E.D IV) I need to also provide Geometry
optimization output(s)... which file is that?
files that i received from Ante Red are:
Mol_red1-info.txt
Mol_red1.inp
Mol_red1-out.p2n
Mol_red1-out.pdb
Mol_red1.pdb
/Urszula
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Donnerstag, 10. November 2011 18:59
An: AMBER Mailing List
Betreff: Re: [AMBER] problems in reading linrary/tleap
Dear Urszula,
You have two atoms with the same name in the residue 5 of pep3.pdb
ATOM 22 N PHO E 5 30.294 0.758 -22.594 0.00 0.00
N1+
ATOM 23 CA PHO E 5 29.832 1.167 -23.909 0.00 0.00
C
ATOM 24 CB PHO E 5 30.689 0.518 -24.987 0.00 0.00
C
ATOM 25 CG PHO E 5 32.070 1.084 -25.097 0.00 0.00
C
ATOM 26 CD1 PHO E 5 32.311 2.224 -25.842 0.00 0.00
C
ATOM 27 CE1 PHO E 5 33.601 2.738 -25.963 0.00 0.00
C
ATOM 28 CZ PHO E 5 34.661 2.109 -25.339 0.00 0.00
C
ATOM 29 O PHO E 5 35.903 2.606 -25.450 0.00 0.00
O
ATOM 30 CE2 PHO E 5 34.433 0.967 -24.601 0.00 0.00
C
ATOM 31 CD2 PHO E 5 33.140 0.457 -24.486 0.00 0.00
C
ATOM 32 C PHO E 5 28.397 0.710 -24.103 0.00 0.00
C
ATOM 33 O PHO E 5 28.027 -0.391 -23.700 0.00 0.00
O
atoms no 29 & 33...
In the concept of a force field library, two atoms cannot bear the
same name in a given residue (obviously, two atoms belonging to two
different residues can share the same name).
regards, Francois
> Dear amber users,
>
> I have still some problem with my files when loading to the xleap,
>
> what i do:
>
> loadoff PHO.lib
> Loading library: ./PHO.lib
> Loading: PHO
>> x = loadpdb pep3.pdb
> Loading PDB file: ./pep3.pdb
> Enter zPdbReadScan from call depth 0.
> -- residue 5: duplicate [ O] atoms (total 2)
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>> check x
> Checking 'x'....
> WARNING: There is a bond of 7.276419 angstroms between:
> ------- .R<PHO 5>.A<CZ 14> and .R<PHO 5>.A<O 15>
> WARNING: The unperturbed charge of the unit: 1.001000 is not zero.
> Warning: Close contact of 1.408529 angstroms between .R<GLY 4>.A<O
> 7> and .R<PHO 5>.A<H1 3>
>
> Does anyone can help me with that?
>
> the lib and pdb files are attached...
>
> thank you in advance
>
> Urszula
>
>
>
> ________________________________________
> Von: FyD [fyd.q4md-forcefieldtools.org]
> Gesendet: Dienstag, 8. November 2011 15:07
> An: AMBER Mailing List
> Betreff: Re: [AMBER] problems in reading molecule in tleap/xleap
>
> Urszula,
>
>> I have changed the atom names and residue but still getting errors:
>
> You did not changed the residue name: the PHO residue does not exist
> in the .lib file; instead you have x...
>
> regards, Francois
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Thu Nov 17 2011 - 08:00:03 PST
