Hi,
I am sure you must have done it. But still asking:
loadamberprep urea.prepin
loadamberparams frcmod.urea
savepdb URE urea.pdb
Here you have not mentioned the* loadpdb* . Have you done that? have you
loaded your pdb as URE before saving it. Can you explain me the same.
Hirdesh
On Wed, Feb 23, 2011 at 12:16 PM, subrata paul <paul.subrata34.gmail.com>wrote:
> 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 - 23:30:04 PST
