AMBER Archive (2009)

Subject: RE: [AMBER] database

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Fri Sep 18 2009 - 14:10:19 CDT

Thank you so much Prof. Case. The "pennie dropped" as they say when I throughly read your email. You were correct. The solution was making my mol2 one residue, calling it P2M, and then coordinating that with how I introducted it into leap containing the newdCTP.pdb file with residue P2M. I took my files and wrote leap.in as:

P2M=loadmol2 newdCTP.mol2
DNA_pol=loadPdb newdCTP.pdb
Saveamberparm DNA_pol DNA_pol.prmtop and DNA_Pol.inpcrd

Thanks Prof. Case and Franscois for having patience in showing me how to do this!!!

Steve

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf Of case
Sent: Friday, September 18, 2009 1:23 PM
To: AMBER Mailing List
Subject: Re: [AMBER] database

On Fri, Sep 18, 2009, Steve Seibold wrote:
>
> Thanks much Prof Case and Franscois for your comments. I have made my
> newCTP2.mol2 into one residue and opened it up to verify this in leap. I
> then once again tried to open my newdCTP3.pdb to match atom types. Once
> again it failed. None of the atoms were recognized same as before.

In your leap.in file, you don't really understand what the leap variables do.
Here is the leap.in file you attached:

#source leaprc.ff03
#source leaprc.gaff
FOO = loadmol2 newdCTP2.mol2
#sus=loadPDB newdCTP3.pdb
#addIons dna Na+ 0
#solvateOct dna TP3 12
#saveamberparm dna DNA_Pol.prmtop DNA_Pol.inpcrd

(I' amm assuming that most of the comment lines were not actually there in
real calculations.)

In line 3, "FOO" is whatever residue name you want to associate with your
unit. In your case, you want this to be "PM2", not "FOO".

In line 4, "sus" will be the name of the leap unit that has the triphosphate
molecule. The variable in line5 ("dna") will be what you add ions to: it
needs to be the same as the unit variable on line 4.

Here is a leap.in file that should be more what you want:

source leaprc.ff03
source leaprc.gaff
PM2 = loadmol2 newCTP2.mol2
x=loadPDB newdCTP3.pdb
addIons x Na+ 0
solvateOct x TP3 12
saveamberparm x DNA.prmtop DNA.inpcrd
quit

However, the newdCTP2.mol2 file is badly mangled. When I try to read this
file into leap, I get a "fatal error:" message. Your file has missing lines;
it still thinks there are four residues, etc. Plus, the atom types are not
gaff atom types, which may or may not be what you want, but you were loading
gaff.dat. I suggest starting from your single-residue pdb file, using
antechamber to create the mol2 file, then using *that* mol2 file in place of
the one you have.

...good luck...dac

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