AMBER Archive (2006)

Subject: Re: AMBER: generating parameters for the NADH analogue H4NAD

From: Vlad Cojocaru (
Date: Thu Feb 23 2006 - 12:53:30 CST


I will try to answer shortly to your questions.

1. You may edit your structure directly in Leap manually by modifying
the atom types (Select-Edit selected atoms). Add-H and Build (leap
manus) would give you an aproximate structure to start with....
Alternatively if you have access to Sybyl or other similar software you
could sketch the molecule and save a mol2 file.....

If you edit with Leap, you can save a pdb file and use it as further
input for antechamber. You can run antechamber to look for missing force
field parameters (see amber manual for details)...... You should check
the antechamber results against your manual atom type definition and of
course proofread the force field parameters given by antechamber agains
the gaff ff...

2. Antechamber should find the missing parameters ... You should read
carefully the amber manual -- antechamber chapter

3. Well, if bond lengths differ, that means atom types differ ... the
assignment of correct atom types should fix this problem ... Antechamber
also checks the bond types in your molecule ... (again see the manual)

4. You can use the AM1-BCC charge model within Antechamber which is
faster ... Alternatively you could perform a RESP charge derivation by
first optimizing the geometry with a QM soft (if you choose latter you
should check the RED program, read the manual and carefully the

If you choose to use Antechamber for charge derivation then, after the
antechamber run, you should get a suitable prep or mol2 file ready for
loading into Leap ..... If you choose to derive RESP charges, the prep
or mol2 files created by antechamber should be edited with the new
charges ..

You have to realize that the parameter derivation is a fairly
complicated process and it would be very hard for someone to write it
here in detail ... so you should really chack the manuals of Amber, RED
and other software before asking such a question ... Without reading
those before, my answer (I believe other answers also) is probably


Simon Whitehead wrote:

>Dear amber users,
>I am trying to generate parameters for an analogue of NADH called H4NAD (tetraNAD) which is one the substrates of the enzyme i am running simulations on (AMBER 8). However, I have some questions about how i should go about it using antechamber starting with a pdb file of NADH;
>1) How do i modify the pdb to add in the additional hydrogens and alter the hybridisation states of the carbons in the nicotinamide ring?
>2) What can i do if GAFF is not able to provide certain parameters for the molecule?
>3) Some of the carbon-carbon bond lengths differ from NADH so would i need to say then minimise this structure in order to correct the geometry or would this simply occur when i perform my minimisations on the entire system prior to running dynamics?
>4) Which charge method would be the most suitable considering the fact that the molecule has about 70 atoms and also are there any specific variables i should be aware of?
>I appreciate i am asking quite a lot here but, I have no experience of generating my own parameters but would like to generate a realistic model because i`m aiming to study the motions of the substrate and interacting active site residues, compared to the physiological substrate, in some detail.
>Kindest regards and thanks in advance
>Simon whitehead
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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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