- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Yuhui Cheng <amberuser3.yahoo.com>

Date: Wed, 25 Aug 2004 17:35:13 -0700 (PDT)

Thanks a lot. I found the manual you mentioned.

Yuhui

--- Lihua Wang <lhw.broyde.nyu.edu> wrote:

*> Hi Yuhui,
*

*>
*

*> I think the reason for your confusion is that
*

*> instructions on how to make
*

*> a prep file has been abridged from the amber manual
*

*> since version 6.
*

*> There is a special section dedicated to topology,
*

*> atom type designation in
*

*> the amber5 manual (the PREP module). It is too long
*

*> for me to present the
*

*> whole section here, but one principle of the
*

*> parameters is that "loop
*

*> closing bonds are not counted as connections when
*

*> assigning M, E, S, B, 3,
*

*> 4,5,6 topological types".
*

*>
*

*> I personally think that section is very important to
*

*> users because as of
*

*> the current version (amber8), the antechamber
*

*> doesn't seem to be able to
*

*> generate prep file for residues. So users still have
*

*> to manually prepare
*

*> the prep file by hand (and I don't see an easy way
*

*> to automate this). So
*

*> including the instructions on how to prepare a prep
*

*> file (with examples,
*

*> as in amber5 manual) is extremely important. If you
*

*> have access to the
*

*> amber5 manual, check out pages 76-85 of volume 2. It
*

*> was very clearly
*

*> described.
*

*>
*

*> Best,
*

*>
*

*> Lihua Wang
*

*>
*

*> On Wed, 25 Aug 2004, Yuhui Cheng wrote:
*

*>
*

*> > Date: Wed, 25 Aug 2004 16:46:36 -0700 (PDT)
*

*> > From: Yuhui Cheng <amberuser3.yahoo.com>
*

*> > Reply-To: amber.scripps.edu
*

*> > To: amber.scripps.edu
*

*> > Subject: AMBER: About tree structure of TRP
*

*> residue
*

*> >
*

*> > Hi, all,
*

*> > Did any one notice that tree structure of TRP
*

*> > amino acid in amber8?
*

*> > In $AMBERHOME/dat/leap/prep/all_amino02.in, it
*

*> > looks like:
*

*> > ........
*

*> > TRYPTOPHAN
*

*> >
*

*> > TRP INT 1
*

*> > CORR OMIT DU BEG
*

*> > 0.00000
*

*> > 1 DUMM DU M 0 -1 -2 0.000
*

*> 0.000
*

*> > 0.000
*

*> > 2 DUMM DU M 1 0 -1 1.449
*

*> 0.000
*

*> > 0.000
*

*> > 3 DUMM DU M 2 1 0 1.522
*

*> 111.100
*

*> > 0.000
*

*> > 4 N N M 3 2 1 1.335
*

*> 116.600
*

*> > 180.000
*

*> > 5 H H E 4 3 2 1.010
*

*> 119.800
*

*> > 0.000
*

*> > 6 CA CT M 4 3 2 1.449
*

*> 121.900
*

*> > 180.000
*

*> > 7 HA H1 E 6 4 3 1.090
*

*> 109.500
*

*> > 300.000
*

*> > 8 CB CT 3 6 4 3 1.525
*

*> 111.100
*

*> > 60.000
*

*> > 9 HB2 HC E 8 6 4 1.090
*

*> 109.500
*

*> > 300.000
*

*> > 10 HB3 HC E 8 6 4 1.090
*

*> 109.500
*

*> > 60.000
*

*> > 11 CG C* S 8 6 4 1.510
*

*> 115.000
*

*> > 180.000
*

*> > 12 CD1 CW B 11 8 6 1.340
*

*> 127.000
*

*> > 180.000
*

*> > 13 HD1 H4 E 12 11 8 1.090
*

*> 120.000
*

*> > 0.000
*

*> > 14 NE1 NA B 12 11 8 1.430
*

*> 107.000
*

*> > 180.000
*

*> > 15 HE1 H E 14 12 11 1.010
*

*> 125.500
*

*> > 180.000
*

*> > 16 CE2 CN S 14 12 11 1.310
*

*> 109.000
*

*> > 0.000
*

*> > 17 CZ2 CA B 16 14 12 1.400
*

*> 128.000
*

*> > 180.000
*

*> > 18 HZ2 HA E 17 16 14 1.090
*

*> 120.000
*

*> > 0.000
*

*> > 19 CH2 CA B 17 16 14 1.390
*

*> 116.000
*

*> > 180.000
*

*> > 20 HH2 HA E 19 17 16 1.090
*

*> 120.000
*

*> > 180.000
*

*> > 21 CZ3 CA B 19 17 16 1.350
*

*> 121.000
*

*> > 0.000
*

*> > 22 HZ3 HA E 21 19 17 1.090
*

*> 120.000
*

*> > 180.000
*

*> > 23 CE3 CA B 21 19 17 1.410
*

*> 122.000
*

*> > 0.000
*

*> > 24 HE3 HA E 23 21 19 1.090
*

*> 120.000
*

*> > 180.000
*

*> > 25 CD2 CB E 23 21 19 1.400
*

*> 117.000
*

*> > 0.000
*

*> > 26 C C M 6 4 3 1.522
*

*> 111.100
*

*> > 180.000
*

*> > 27 O O E 26 6 4 1.229
*

*> 120.500
*

*> > 0.000
*

*> > ...............
*

*> > The tree label of atom CE2 is "S", and CD2 is
*

*> > "E". That means there is no bond between CE2 and
*

*> CD2,
*

*> > Also no bond between CD2 and CG. But obviously,
*

*> it's
*

*> > not correct. I'm totally confused.
*

*> >
*

*> > Thanks,
*

*> > Yuhui
*

*> >
*

*> >
*

*> >
*

*> > _______________________________
*

*> > Do you Yahoo!?
*

*> > Express yourself with Y! Messenger! Free. Download
*

*> now.
*

*> > http://messenger.yahoo.com
*

*> >
*

*>
*

-----------------------------------------------------------------------

*> > The AMBER Mail Reflector
*

*> > To post, send mail to amber.scripps.edu
*

*> > To unsubscribe, send "unsubscribe amber" to
*

*> majordomo.scripps.edu
*

*> >
*

*>
*

-----------------------------------------------------------------------

*> The AMBER Mail Reflector
*

*> To post, send mail to amber.scripps.edu
*

*> To unsubscribe, send "unsubscribe amber" to
*

*> majordomo.scripps.edu
*

*>
*

_______________________________

Do you Yahoo!?

Win 1 of 4,000 free domain names from Yahoo! Enter now.

http://promotions.yahoo.com/goldrush

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Thu Sep 02 2004 - 01:15:11 PDT

Date: Wed, 25 Aug 2004 17:35:13 -0700 (PDT)

Thanks a lot. I found the manual you mentioned.

Yuhui

--- Lihua Wang <lhw.broyde.nyu.edu> wrote:

-----------------------------------------------------------------------

-----------------------------------------------------------------------

_______________________________

Do you Yahoo!?

Win 1 of 4,000 free domain names from Yahoo! Enter now.

http://promotions.yahoo.com/goldrush

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Thu Sep 02 2004 - 01:15:11 PDT

Custom Search