AMBER Archive (2008)

Subject: Re: AMBER: Query about the charge of atoms in the parmtop file

From: Alan (alanwilter_at_gmail.com)
Date: Fri Jul 25 2008 - 14:13:43 CDT

Dears,

My 2 cents here about leaprc.ff03.r1 and leaprc.ff03

If you copy and past the lines below, I would to understand why I have this:

ERROR: The unperturbed charge of the unit: 0.800046 is not integral.
WARNING: The unperturbed charge of the unit: 0.800046 is not zero.

(it's trying to put only 3 Cl- when should be 4)

But, if your replace leaprc.ff03.r1 by leaprc.ff03, charges is zero as
it should be.

wget -c "http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1BVG"
-O 1BVG.pdb
sed s/HIS\ /HID\ /g 1BVG.pdb | sed s/H1\ \ PRO/H3\ \ PRO/g | grep
'ATOM ' >| prot.pdb
tleap
verbosity 1
source leaprc.ff03.r1
prot = loadpdb prot.pdb
addions prot Cl- 0
saveamberparm prot prot.top prot.xyz

Besides, should I be concerned about this other warnings?:

Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2

Many thanks in advance.

Alan

On Thu, Jul 24, 2008 at 2:09 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> I would also think carefully about whether GLYCAM06 is compatible with ff03-
> certainly they do not use the same charge model. You should be ok if you can
> find papers that have validated the combination and show eg that Hbonds between
> the 2 param sets are similar to those internally. Maybe not a major issue, but
> it's kind of like mixing charmm and amber parameters together- who knows
> what you will get? One should not assume. in my opinion, that all
> "Amber" force
> fields are the same and therefore can be mixed and matched. Keep a careful
> eye on things like the charge model. My feeling is that simulations using
> DNA, RNA, or other force fields using the 6-31G*/HF charge derivation procedure
> should be kept with protein sets that do the same. I recommend ff99SB, but
> with full disclore I have to say that I'm biased because that is from my lab.
> However, the reason we made that force field was to have a good parameter
> set that still had the same charge model as all of the non-protein
> param sets that
> people have developed over the years.
> carlos
>
> On Thu, Jul 24, 2008 at 8:49 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>> Hi Madhurima,
>>
>>> I'm using leaprc.ff03 for protein and leaprc.GLYCAM_06 for the
>>> carbohydrate. Now the selective part of the *.parmtop file generated
>>> for my system is given below
>>>
>>> %FLAG CHARGE
>>> %FORMAT(5E16.8)
>>> 3.28183623E+00 3.50050383E+00 3.50050383E+00 3.50050383E+00
>>> 6.70580640E-01
>>>...
>>> So the N terminal end of the protein is ASN. Now in "all_aminont03.in"
>>> file it is given
>>>...
>>> So for terminal N atom of ASN (in parmtop file) charge =
>>> 3.28183623E+00/18.2223 = 0.18009 which is not equal to the value of
>>> -0.669106 given in the above table.
>>
>> Last time I tried out FF03 for some reason there were no terminal residues
>> defined so all regular residues used the FF03 charges while the terminal
>> residues used FF99 (FF94) style charges. This was a concous decision made as
>> part of the FF03 development - I.e. they only refitted the charges on
>> regular residues. Was this a valid decision, in my opinion probably not, but
>> maybe there is evidence that it is perfectly okay, I would ask the FF03
>> developers for their opinions on that.
>>
>> What you are seeing here is likely that behavior, I.e. the N charge here
>> probably matches that of NASN from FF94. In fact if you take a look in the
>> leaprc.ff03 leap file you will see exactly this:
>>
>> loadOff all_aminoct94.lib
>> loadOff all_aminont94.lib
>> loadOff all_amino03.lib
>>
>> So leap does exactly what is asked of it. All the C and N terminals use FF94
>> charges while all the standard residues use FF03 charges.
>>
>> If you check the amber 10 cmd directory you will see there is also a
>> leaprc.ff03.r1 file (which I just discovered myself). This does the
>> following:
>>
>> loadOff all_aminoct03.lib
>> loadOff all_aminont03.lib
>> loadOff all_amino03.lib
>>
>> Which will then use the FF03 CT and NT charges. Interestingly a paragraph on
>> this just appeared in the AMBER tools manual:
>>
>> "The original model used the old (ff94) charge scheme for N- and C-terminal
>> amino acids.
>> This was what was distributed with Amber 9, and can still be activated by
>> using leaprc.ff03.
>> More recently, new libraries for the terminal amino acids have been
>> constructed, using the same
>> charge scheme as for the rest of the force field. This newer version (which
>> is recommended for
>> all new simulations) is accessed by using leaprc.ff03.r1."
>>
>> I don't blame you for missing this - I just found it myself. But it looks
>> like if you use the .r1 file you should get the charges you expect.
>>
>> Good luck,
>> Ross
>>
>>
>> /\
>> \/
>> |\oss Walker
>>
>> | Assistant Research Professor |
>> | San Diego Supercomputer Center |
>> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
>> | http://www.rosswalker.co.uk | PGP Key available on request |
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>> be read every day, and should not be used for urgent or sensitive issues.
>>
>>
>>
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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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