Dear Amber users,
I can resolve the following problems by adding
remove x x.1.45
remove x x.1.46
in leap input file of step-2.
However, I cannot understand why I cannot prepare parameter file simply.
I am most grateful if anyone answer the question.
Yours sincerely,
Ikuo Kurisaki
Dear Amber users,
I am most grateful if anyone answer my question.
I am now trying to perform MD calculations for GTP.
By usege of tLEaP in AmberTools, the paramter files were prepared as following:
Step-1: preparing GTP-solution
>source leaprc.ff99SB
>loadamberprep GTP.prep
>loadamberparams frcmod.phos
>x = gtp
>solvatebox x TIP3PBOX 10
>savepdb x solute.pdb
Step-2: preparing parameter files with specific water model
>source leaprc.ff99SB
>WAT = SPC
>loadAmberParams frcmod.spce
>loadamberprep GTP.prep
>loadamberparams frcmod.phos
>x = loadpdb solute.pdb
>setBox x centers
>saveamberparm x gtp_10A_SPC.prmtop gtp_10A_SPC.prmcrd
>quit
Here, I used prep file and frcmod file downloaded from Amber Home Page.
However, I encountered a problem in step-2 when loading the PDB file, "solute.pdb".
The error message,
Created a new atom named: O2* within residue: .R<gtp 1>
Created a new atom named: HO*2 within residue: .R<gtp 1>
.
.
.
Added missing heavy atom: .R<gtp 1>.A<O2' 43>
.
.
FATAL: Atom .R<gtp 1>.A<O2* 45> does not have a type.
FATAL: Atom .R<gtp 1>.A<HO*2 46> does not have a type.
.
.
was shown and paramer files cannot be saved.
I would like to know how to circumvent this error.
You would think that I should do in 1 step.
Of coures, I tried it.
I found that I cannot
If I use waterbox (e.g. )
It is important for us to use waterbox to keep whole watar molecule number
among different water model solvent.
Thank you for kind support,
Ikuo Kurisaki
$B7*:j0J5WCK(B
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E-mail: kurisaki.fc.ritsumei.ac.jp
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$B7*:j0J5WCK(B
$BN)L?4[Bg3X.8L?2J3XIt.8L?>pJs3X2J(B
$B9b66BnLi8&5f<<=jB0(B $BGn;N8&5f0w(B
$B")(B525-8577 $B<"2l8)ApDE;TLnO)El(B1-1-1
E-mail: kurisaki.fc.ritsumei.ac.jp
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Received on Wed Aug 04 2010 - 21:00:03 PDT
