Dear amber user,
I want to simulate Urea solution.I had made urea.prepin and frcmod.urea file
urea.
loadamberprep urea.prepin
loadamberparams frcmod.urea
savepdb URE urea.pdb
after saving the pdb file I used Packmol to creat 100 urea molecule in a box
.
after saving 100urea.pdb by packmol.
ureabox=loadpdb 100urea.pdb
but following error are showing..
(Residue 0: URE, Terminal/last, was not found in name map.)
Unknown residue: URE number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
(Residue 1: URE, Terminal/last, was not found in name map.)
Unknown residue: URE number: 1 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
(Residue 2: URE, Terminal/last, was not found in name map.)
Unknown residue: URE number: 2 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
(Residue 3: URE, Terminal/last, was not found in name map.)
Unknown residue: URE number: 3 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
(Residue 4: URE, Terminal/last, was not found in name map.)
Unknown residue: URE number: 4 type: Terminal/last
................
Creating new UNIT for residue: URE sequence: 1
Created a new atom named: O within residue: .R<URE 1>
Created a new atom named: C within residue: .R<URE 1>
Created a new atom named: N2 within residue: .R<URE 1>
Created a new atom named: H3 within residue: .R<URE 1>
Created a new atom named: H4 within residue: .R<URE 1>
Created a new atom named: N1 within residue: .R<URE 1>
Created a new atom named: H1 within residue: .R<URE 1>
Created a new atom named: H2 within residue: .R<URE 1>
Creating new UNIT for residue: URE sequence: 2
Created a new atom named: O within residue: .R<URE 2>
Created a new atom named: C within residue: .R<URE 2>
Created a new atom named: N2 within residue: .R<URE 2>
Created a new atom named: H3 within residue: .R<URE 2>
Created a new atom named: H4 within residue: .R<URE 2>
Created a new atom named: N1 within residue: .R<URE 2>
Created a new atom named: H1 within residue: .R<URE 2>
Created a new atom named: H2 within residue: .R<URE 2>
Creating new UNIT for residue: URE sequence: 3
...........................
saveamberparm ureabox ureabox.prmtop ureabox.inpcrd
Checking Unit.
FATAL: Atom .R<URE 1>.A<O 1> does not have a type.
FATAL: Atom .R<URE 1>.A<C 2> does not have a type.
FATAL: Atom .R<URE 1>.A<N2 3> does not have a type.
FATAL: Atom .R<URE 1>.A<H3 4> does not have a type.
FATAL: Atom .R<URE 1>.A<H4 5> does not have a type.
FATAL: Atom .R<URE 1>.A<N1 6> does not have a type.
FATAL: Atom .R<URE 1>.A<H1 7> does not have a type.
FATAL: Atom .R<URE 1>.A<H2 8> does not have a type.
FATAL: Atom .R<URE 2>.A<O 1> does not have a type.
FATAL: Atom .R<URE 2>.A<C 2> does not have a type.
FATAL: Atom .R<URE 2>.A<N2 3> does not have a type.
FATAL: Atom .R<URE 2>.A<H3 4> does not have a type.
FATAL: Atom .R<URE 2>.A<H4 5> does not have a type.
FATAL: Atom .R<URE 2>.A<N1 6> does not have a type.
FATAL: Atom .R<URE 2>.A<H1 7> does not have a type.
FATAL: Atom .R<URE 2>.A<H2 8> does not have a type.
FATAL: Atom .R<URE 3>.A<O 1> does not have a type.
FATAL: Atom .R<URE 3>.A<C 2> does not have a type.
FATAL: Atom .R<URE 3>.A<N2 3> does not have a type.
Why this type of error are coming??
How I solve this??
thanking you
subrata
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Received on Tue Feb 22 2011 - 23:00:04 PST
