AMBER Archive (2009)

Subject: Re: [AMBER] Pentane UA model

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Sep 22 2009 - 02:02:50 CDT

Aneesh,

> I would like to use United atom model of n-pentane for
> simulation. Can anyone have United atom force field for n-pentane. Im using
> Amber 9.0 version

If you use R.E.D. & provide the P2N file (I added below as input), you
will get an united-atom force field library in the Tripos mol2 file
format for Pentane. With R.E.D. you will be able to generate various
RESP or ESP charge models. Obviously, different approaches could be
followed here...

Take always a look at the RRMS value of the charge fitting step. See
R.E.DD.B. as well for an example of alkane available. The RRMS of the
fit is also reported.
http://q4md-forcefieldtools.org/REDDB/projects/W-43/

regards, Francois

REMARK TITLE Pentane
REMARK CHARGE-VALUE 0
REMARK MULTIPLICITY-VALUE 1
REMARK
REMARK REORIENT 1 5 8 | 8 5 1
REMARK
REMARK INTRA-MCC 0.0 | 2 | Remove
REMARK INTRA-MCC 0.0 | 3 | R
REMARK INTRA-MCC 0.0 | 4 | R
REMARK INTRA-MCC 0.0 | 6 | R
REMARK INTRA-MCC 0.0 | 7 | R
REMARK INTRA-MCC 0.0 | 9 | R
REMARK INTRA-MCC 0.0 | 10 | R
REMARK INTRA-MCC 0.0 | 12 | R
REMARK INTRA-MCC 0.0 | 13 | R
REMARK INTRA-MCC 0.0 | 15 | R
REMARK INTRA-MCC 0.0 | 16 | R
REMARK INTRA-MCC 0.0 | 17 | R
REMARK ***
ATOM 1 CT1 PTN 1 10.674 -4.966 -0.012 C1 # ***:
ATOM 2 H11 PTN 1 11.444 -5.560 0.221 H11 # not equivalenced
ATOM 3 H12 PTN 1 10.721 -4.130 0.534 H12 # as all set to 0
ATOM 4 H13 PTN 1 10.714 -4.733 -0.984 H13
ATOM 5 CT2 PTN 1 9.387 -5.680 0.278 C2
ATOM 6 H21 PTN 1 9.337 -6.516 -0.268 H21
ATOM 7 H22 PTN 1 9.349 -5.914 1.250 H21
ATOM 8 CT3 PTN 1 8.231 -4.788 -0.065 C3
ATOM 9 H31 PTN 1 8.262 -4.559 -1.038 H31
ATOM 10 H32 PTN 1 8.287 -3.949 0.476 H32
ATOM 11 CT2 PTN 1 6.944 -5.494 0.244 C4
ATOM 12 H41 PTN 1 6.919 -5.728 1.216 H41
ATOM 13 H42 PTN 1 6.882 -6.330 -0.302 H42
ATOM 14 CT1 PTN 1 5.789 -4.595 -0.082 C5
ATOM 15 H51 PTN 1 5.810 -4.361 -1.054 H51
ATOM 16 H52 PTN 1 5.854 -3.759 0.464 H52
ATOM 17 H53 PTN 1 4.931 -5.064 0.130 H53
CONECT 1 2 3 4 5
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1 6 7 8
CONECT 6 5
CONECT 7 5
CONECT 8 5 9 10 11
CONECT 9 8
CONECT 10 8
CONECT 11 8 12 13 14
CONECT 12 11
CONECT 13 11
CONECT 14 11 15 16 17
CONECT 15 14
CONECT 16 14
CONECT 17 14
END

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