AMBER Archive (2009)

Subject: RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot

From: xueqin pang (pangxueqintea_at_yahoo.com.cn)
Date: Tue Jun 16 2009 - 02:57:25 CDT

Dear Francois,

Thanks very much for your replay.

To your questions:

1. The input conformation is one molecular from the lipid membrane pdb (128 pre-stabled dppc pdb) (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies dppc128.pdb), I just take coordinates of the first dppc molecular out and then add H atoms by Leap in amber. surprisingly, after optimizing by G03 (HF/6-31G* freq SCF=Tight Pop=MK IOp(6/33=2)), the tail of the DPPC changed a lot (please check the attachments).
Actually, the conformation of different moleculars in the membrane pdb may be also different from others.

2.I get the RESP charges by RESP module of AMBER10 form Gauss output
(antechamber -i g.out -fi gout -o test_resp.mol2 -fo mol2 -c resp)
or by:
(resgen -i test.ac -o test.respin1 -f resp1;
respgen -i test.ac -o tesp.respin2 -f resp1;
resp -O -i test.respin1 -o test.respout1 -e test.esp -t qout_stage1
resp -O -i test.respin2 -o test.respout2 -e test.esp?-q qout_stage1 -t qout_stage2
antechanber -i test.ac -fi ac -o test_resp.ac -fo -c rc -cf qout_stage2)?
So there is no selection of the conformation for MEP computation.

3.I read the amber forum about calculating the atomic charges by RESP methods and now I am going to try R.E.D. But before moving to R.E.D., I still have some confusions to figure out.

My questions are:

a. Can I use the initial structure of DPPC to calculate the MEP and then fit the MEP to get atomic charges within R.E.D. G03 frequency calculation of the initial structure reveals three imaginary frequencies.

b. If the initial structure can't be adopted to evaluate the MEP, is the optimized structure reasonable for the task?
In my opinion, the equilibrium structures of DPPC should not change very much during MD simulation, so the conformation used to derive the partial charges should be similar to the equilibrium structure. If the conformation changes too much after optimization, the atomic charges won't represent the electrostatic interactions during md simulaiton.

c. If neither is correct, what parameters should be used to optimize the initial structure in order to calculate the MEP With restraints or taking the solvent effect into account?

Now this is the main question I am worrying about. I request your help and suggestions on this work.

Thanks so much.

=============================================================================================================
Pang Xueqin
State Key Laboratory of Molecular Reaction Dynamics
Dalian Institute of Chemical Physics
Chinese Academy of Sciences.
Tel: 0411-84379352 Fax: 0411-84675584
http://www.english.dicp.ac.cn/
=============================================================================================================

发件人: FyD <fyd_at_q4md-forcefieldtools.org>
主题: Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot
收件人: "amber_at_ambermd.org" <amber_at_ambermd.org>
日期: 2009年6月12日,周五,上午2:59

Dear Xueqin Pang,

> I聽intend to get the partial charges of DPPC (C40H80NO8P) with RESP  after optimization with Gauss. However the output of Gauss for the  lipid (dppc) differs a lot from the input聽 conformation.

What is this input conformation ? Where does it come from ?

> What is more, after stimulating with AM1-BCC and RESP,聽聽the  given聽partial charges of the gout is quite different, espancially  for the N atom, which is .-0.58700 in AM1-BCC, but 0.060945 from RESP.

Difficult to answer here.

Are you sure the way for deriving the RESP charges for your molecule is correct ? Did you use R.E.D. ? You need a P2N input file: I can help you to prepare it if you have problems for that.

> So do聽you have聽any suggestions on聽what to do with Gauss. and which  partial change should聽 I use?聽聽

>From what I quickly saw your input is huge... Based on which criteria did you select the conformation used in MEP computation ? Based on luck ?

Then, the charges of the Hs of a methyl group as well as those of the methylene have to be equivalenced. The charges of the ammonium methyls have to be equivalenced as well... Charge equivalecing seems to be correct for RESP charges (although I did not check carefully) but not for AM1-BCC. Why ?

regards, Francois

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