AMBER Archive (2006)

Subject: RE: AMBER: printing Amber VdW radii as separate column in pdb files

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Apr 10 2006 - 11:03:18 CDT

In these situations I always recommend that one goes and RTS's (Read the
source...)

You will find ambpdb.f in $AMBERHOME/src/etc.

It is a really simple fortran code, is all in one file and is only 774 lines
long... Easy, you don't even need to know Fortran to follow it...

Now if you trace it through you will find a routine called GENPDB. Inside
this if you search for -pqr you will see the following line:

            else if (arg1.eq.'-pqr') then
              WRITE(NF,81) K,atnam,LBRES(J),J_print,
     . (C(JC+M),M=1,3),chg(k),elrad(itype)

So, you can see that the radii are written from the array elrad(...). So
search through the code for elrad and what do you find:

      dimension elrad(15)
c
c from Sitkoff, Sharp & Honig, PARSE values, J. Phys. Chem. 98:1978(1994)
c
c data elrad/2.0, 1.4, 1.0, 1.5, 1.0, 0.0, 1.7, 1.85, 0.0, 0.0, 0.0,
c . 0.0, 0.0, 0.0, 1.0/
c
c Bondi radii, from Huheey, Inorganic Chemistry: Principles of Structure
c and Reactivity, 2nd ed. p. 232.
c
      data elrad/1.85, 1.5, 1.0, 1.55, 1.0, 0.0, 1.7, 1.8, 0.0, 0.0,
     . 0.0, 0.0, 0.0, 0.0, 1.2/

It is defined in a data statement. So ambpdb doesn't read the radii from the
prmtop file at all, it is hard wired into the code. Hence the behaviour you
are seeing.

Thus without modification of the code ambpdb cannot do what you want. You
should try ptraj I think this may do it.

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Vlad Cojocaru
> Sent: Monday, April 10, 2006 08:43
> To: amber_at_scripps.edu
> Subject: Re: AMBER: printing Amber VdW radii as separate
> column in pdb files
>
> Dear Harianto,
>
> There is only one %FLAG RADII in the top file .... and all hydrogens
> have 1.30000000E+00 radii, there isnt any 1.20000000E+00 number in my
> top file so I dont know why ambpdb -pqr prints 1.200 for each
> H atom ...
>
> ptraj, trajout dumpq works fine (I forgot about about it).... thanks
>
> vlad
>
>
> harianto wrote:
>
> >Dear Vlad,
> >By default, "ambpdb -pqr" command prints the 'PBRadii Bondi'
> set, but in
> >your top file they look like 'PBradii mBondi2'.
> >You can use ptraj option 'trajout file.out PDB [dumpq/PARSE]', for
> >example, to print out the PDB with radii and charge columns.
> >Does that help ?
> >
> >Regards,
> >Harianto.
> >
> >On Mon, 2006-04-10 at 16:41 +0200, Vlad Cojocaru wrote:
> >
> >
> >>Dear amber users,
> >>
> >>In the RADII section of the topology file, Born radii are
> printed (see
> >>SECTION 1 below).... Now if I create a pqr file (ambpdb
> -pqr) from this
> >>topology file I get on the radii column the output shown below in
> >>SECTION 2. So, my first question is why the radii of the
> hydrogens are
> >>different in the resulting pqr file comparing to the
> topology file...
> >>
> >>And second question (actually the most important): Is there a way to
> >>print out the VdW radii from the Amber ff (specified in the
> parm99.dat
> >>lines 663 to 708) as a separate column in a pdb file created from an
> >>AMBER top and crd files?
> >>
> >>Thank you very much,
> >>
> >>Best wishes
> >>vlad
> >>
> >>------------------------------------------------------------
> ----------------------
> >>SECTION 1:
> >>
> >>%FLAG RADII
>
> >>%FORMAT(5E16.8)
>
> >> 1.55000000E+00 1.30000000E+00 1.30000000E+00
> 1.30000000E+00 1.70000000E+00
> >> 1.30000000E+00 1.30000000E+00 1.70000000E+00
> 1.50000000E+00 1.55000000E+00
> >>------------------------------------------------------------
> ---------------------
> >>SECTION 2:
> >>
> >>ATOM 1 N GLY 1 -22.774 -18.746 1.138
> 0.2943 1.550
> >>ATOM 2 H1 GLY 1 -22.400 -17.825 0.958
> 0.1642 1.200
> >>ATOM 3 H2 GLY 1 -23.230 -18.741 2.039
> 0.1642 1.200
> >>ATOM 4 H3 GLY 1 -23.277 -19.057 0.319
> 0.1642 1.200
> >>ATOM 5 CA GLY 1 -21.628 -19.693 1.281
> -0.0100 1.700
> >>ATOM 6 HA2 GLY 1 -21.698 -20.144 2.271
> 0.0895 1.200
> >>ATOM 7 HA3 GLY 1 -21.746 -20.466 0.521
> 0.0895 1.200
> >>ATOM 8 C GLY 1 -20.255 -19.050 1.125
> 0.6163 1.700
> >>ATOM 9 O GLY 1 -19.242 -19.666 1.479
> -0.5722 1.500
> >>ATOM 10 N LYS 2 -20.225 -17.831 0.576
> -0.4359 1.550
> >>------------------------------------------------------------
> ----------------------
> >>
> >>
> >
> >-------------------------------------------------------------
> ----------
> >The AMBER Mail Reflector
> >To post, send mail to amber_at_scripps.edu
> >To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> >
> >
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg, Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
>
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu