[AMBER] How to make parameter files of GTP from PDB file.

From: kurisaki ikuo <kurisaki.fc.ritsumei.ac.jp>
Date: Thu, 05 Aug 2010 12:12:59 +0900 (JST)

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




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E-mail: kurisaki.fc.ritsumei.ac.jp

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Received on Wed Aug 04 2010 - 20:30:04 PDT
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