Dear
ambrer user
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.
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
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
(Residue 1: UEA, Terminal/last, was not found in name map.)
Unknown residue: UEA number: 1 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
(Residue 2: UEA, Terminal/last, was not found in name map.)
Unknown residue: UEA number: 2 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
(Residue 3: UEA, Terminal/last, was not found in name map.)
Unknown residue: UEA number: 3 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
(Residue 4: UEA, Terminal/last, was not found in name map.)
Unknown residue: UEA number: 4 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
(Residue 5: UEA, Terminal/last, was not found in name map.)
Unknown residue: UEA number: 5 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
(Residue 6: UEA, Terminal/last, was not found in name map.)
Unknown residue: UEA number: 6 type: Termina
Why this error are coming*??
*please help me regarding this.
thanking YOU
subrata
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Received on Wed Feb 23 2011 - 03:30:02 PST
