Hi,
> I downloaded tripos1.mol2 file for urea molecule and change the name
> H11_to_H1, H12_to_H2 , H21_to_H3 and H22_to_H4.
why? I might be wrong but you should not need to do that...
> after that converto frcmod.UEA and UEA.prepin
> antechamber -i tripos1.mol2 -fi mol2 -o UEA.prepin -fo prepi
> parmchk -i UEA.prepin -f prepi -o frcmod.UEA
You can use a mol2 file to regenerate another mol2 file
> after convert in to this file..
> xleap -f leaprc.GLYCAM_06
> source leaprc.gaff
> loadamberprep UEA.prepin
> loadamberparams frcmod.UEA
> savepdb UEA uea.pdb
>
> after saving the pdb file I use *packmol* to make 100_urea.pdb
>
> again
> xleap -f leaprc.GLYCAM_06
> source leaprc.gaff
> loadamberparams frcmod.UEA
> aa=loadpdb 100_urea.pdb
>
> after loading the pdb file I got following error..
> Loading PDB file: ./uea_100.pdb
> Enter zPdbReadScan from call depth 0.
> Exit zPdbReadScan from call depth 0.
> Matching PDB residue names to LEaP variables.
> (Residue 0: UEA, Terminal/last, was not found in name map.)
> Unknown residue: UEA number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
[...]
> Why this error are coming*??
I think you need to load the FF library file before to load the PDB file
xleap -f leaprc.GLYCAM_06
source leaprc.gaff
loadamberparams frcmod.UEA
=> load the mol2 file (or prep file)
aa=loadpdb 100_urea.pdb
regards, Francois
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Received on Wed Feb 23 2011 - 07:00:04 PST
