AMBER Archive (2009)

Subject: RE: [AMBER] QQD psuedoatom restraints

From: Titus, Jamie (bairdje) (BAIRDJE_at_UCMAIL.UC.EDU)
Date: Mon Jun 01 2009 - 06:21:19 CDT

Hello,

Oops, sorry. Well the restraint now looks like this after makeDIST_RST:
# 13 LEU QQD 16 LEU QQD 3.61 (#peak 191)
 &rst
  ixpk= 191, nxpk= 0, iat= 226, 277, r1= 1.30, r2= 1.80, r3= 8.01, r4= 8.51, &end

Which shows that the values of r3 and r4 have been modified appropriately. Thanks!

And, somewhat related to the discussion and FYI, I changed my map.DG-AMBER by adding the following lines to the TYR, PHE, HIS, and THR entries (for full CYANA compatibility, and to reflect a few unusual assignments):

PHE and TYR:
MAPPING QD = HD1 HD2
MAPPING QE = HE1 HE2
THR:
MAPPING HG1 = HG1
HI:
MAPPING HE1 = HE1

Jamie
________________________________________
From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of David A. Case [case_at_biomaps.rutgers.edu]
Sent: Friday, May 29, 2009 3:26 PM
To: AMBER Mailing List
Subject: Re: [AMBER] QQD psuedoatom restraints

On Fri, May 29, 2009, Titus, Jamie (bairdje) wrote:
>
> I applied the patch to /usr/local/amber10/src/nmr_aux/prepare_input/makeDIST_RST.c using the following:
> patch -p0 -N < dist.patch
> make -f Makefile_at
      ^^^^^^^^^^^^^^^^

This is wrong: makeDIST_RST is a part of Amber, not AmberTools. So, it looks
like you were probably not running the updated version of makeDIST_RST.

You can just go into $AMBERHOME/src/nmr_aux/prepare_input, and type "make
install". Then you should see differences in the output RST file.

...good luck...dac

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