AMBER Archive (2008)

Subject: Re: Re: Re: Re: AMBER: AdoMet parameterization with antechamber

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Wed Nov 26 2008 - 08:44:27 CST

Dear everyone,

     Maybe I don't say my questions clearly in my last post. After checking the related papers and mannual, I have got answers to some questions in last post. Now the main question is about the torsional interaction in AMBER. I checked the parm99.dat and found the format for torsion as follows:
-----
...
CT-CT-N -C 1 0.50 180.0 -4. phi,psi,parm94
CT-CT-N -C 1 0.15 180.0 -3. phi,psi,parm94
CT-CT-N -C 1 0.00 0.0 -2. JCC,7,(1986),230
CT-CT-N -C 1 0.53 0.0 1. phi,psi,parm94
...
------
As stated in JACS1995v117p5179 "The periodicity of the torsion. A negative value is not used in the calculation but signifies more than one component around a given bond." I don't know what is the role of the parameters in line with negative periodicity. I am trying to find the corresponding code in src/ but failed to understand so many formal parameters in the subroutines...

As I want to use specific amber parameters for the sulfonium group( in supporting material of biochem2002v41p7636) in AMBER10 for AdoMet, any one who can tell me how to prepare them in .frcmod file?

The parameterized torsional constants for sulfonium group are:
-----
Torsional Interaction (Kcal/mol)
                          V1/2 V2/2 V3/2
SP ¨C CT ¨C CT ¨C CT -1.6814 1.0698 -0.0001
SP ¨C CT ¨C CT ¨C H1 0.9529 1.1047 0.0695
SP ¨C CT ¨C CT ¨C O3 3.5661 0.5502 -0.0208
----------

Any one who can give me some suggestions on how to use these parameters in AMBER10?

Any suggestion is greatly appreciated.
Thanks so much for the time.

Have a nice day. 

---
Jeffrey
 

 

>Thanks so much for all the replies. I am sorry that in my last test run and post one hydrogen atom was overlooked by me. Following your instructions, now I can build the parameters of AdoMet with antechamber successfully. Since AdoMet contains a sulfonium group, I am wondering whether gaff can provide stable parameters for the system now? If not, I am going to combine the parameters for sulfonium group in the supporting material of BioChem 2002,41,7636 with the param99.dat to build a full model used in MD simulation. But I still have some questions in the process of the work and need your great help.
>
>1. Is it a reasonable way by using the parm99.dat instead of the gaff.dat to build a new unit in AMBER?  Or should I just use the parameters for sulfonium group in the mentioned paper and the parameters in gaff.dat for the rest of the system? The reason why I want to use parm99.dat is that AdoMet is an combination of MET and part of ADE ( the adenine and the ribose) for which parm99.dat can provide more specific parameters.
>
>2. If the answer in 1 is yes, then the following steps are adopted to finish the job. Firstly, the antechamber was used with the sam.pdb file as the input to get a prep file, sam.prepin. Then the atom types in sam.prepin file were substituted by atom types in parm99.dat and keep the charges calculated by antechamber in the first step unchanged. Finally, the missing parameters relating to the sulfonium group were prepared in a file called sam.frcmod.   Is it ok to do so?
>
>3. It seems that the energy expression of torsional interactions in the paper is different with the one used in AMBER10.
> Et = V1/2*(1+Cos(phi))+V2/2*(1+Cos(2*phi))+V3/2*(1+Cos(3*phi)) in the paper. 
>For example, the parameters for SP-CT-CT-CT interaction in the paper is as follows:
>----------------
>                 Torsional Interaction (Kcal/mol)
>                      V1/2        V2/2        V3/2
>SP ¨C CT ¨C CT ¨C CT  -1.6814       1.0698      -0.0001
>----------------
>Then how to convert the parameters in the paper to the ones used in AMBER10, Vn/2-potential barrier, gamma-phase offset, n-periodicity of the torsion and the number of bond paths?
>
>4. It seems that antechamber produces different charge values for different configurations of AdoMet. Which one should I use?
>
>5. Is there a detailed document for the format and explanation of the amber FF? I am not very clear how to calculate the number of the bond paths in torsion interaction.
>
>Any suggestion is greatly appreciated and thanks so much for your time.
>
>Have a nice day.
>
>-------
>Jeffrey
>
>
>>On Tue, Nov 25, 2008, Jeffrey wrote:
>>> 
>>> Thanks so much for your instruction, David.
>>> 
>>> When running antechamber with all hydrogens, something strage was observed
>>> in the output. As in AdoMet, the sulfur atom is a sulfonium resulting in a
>>> system with 1 net positive charge. But the output message showed that the
>>> net charge was zero...
>>
>>
>>> [c0225 sam]$ antechamber -i sam.pdb -fi pdb -o sam.prepin -fo prepi -c bcc -s 2
>>
>>If you have a net charge, you need to use the "-nc" flag in antechamber.
>>
>>> Total number of electrons: 210; net charge: 0
>>
>>However, since you have 210 electrons in a neutral system, you would have 209
>>electrons with a +1 charge.  But antechamber can only handle closed shell
>>systems with an even number of electrons.
>>
>>Your SAM structure appears to be missing a proton at the O3' position.
>>
>>...dac
>>
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