AMBER Archive (2006)

Subject: Re: AMBER: Compile AMBER 8

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Mon Oct 30 2006 - 11:24:59 CST

Dear hayden,
 
 thanks for your suggetion and help. unfortunetly, I have no gaussian with me. Is there any other ways to do this calculation?
 Thanks again,
 esther B.

HL Eastwood <s0237717_at_sms.ed.ac.uk> wrote: Hullo Esther

Because each residue will delete one H atom, then can
> bind them together. How can I bind these residues together with total
> charge is 0?
>

Unfortunately the problem to which you refer is not an easy one to
solve. In essence it requires running each of the RESP programmes
separately with manually modified input files. I will give you the
procedure that I used some time ago to get neutral charges for a
residue:

1. optimise your residue in gaussian and then perform a single point
calculation (also with gaussian) using the appropriate ESP settings in
the gaussian input section (see amber manual force field section.) NB.
at this stage keep your hydrogens attached!! if you've already got
charges this step won't be necessary.

2. Convert your output from step 1 to an "antechamber" format (see
antechamber options for this).

3. run espgen on your gaussian output file to get your ESP points as follows:
             espgen -i -o

4. run respgen to generate your resp input files:
             respgen -i -o -f resp1
             respgen -i -o -f resp2

(NB when you run respgen you must do so sequentially, first using the
flag "resp1" and then the flag "resp2". This step will give rise to 2
resp input files which then need to be modified manually.

The first of the 2 should look something like this:

Resp charges for organic molecule

  &cntrl

  nmol = 1,
  ihfree = 1,
  ioutopt = 1,

  &end
     1.0
Resp charges for organic molecule
    -1 39
     6 0
     8 0
     1 0
     1 0
     1 0
     6 0
     6 0
     6 0
     6 0
     6 0
     6 0
     7 0
     8 0
     8 0
     8 0
     1 0
     1 0
     1 0
     1 0
     1 0
     1 0
     6 0
     1 0
     1 0
     1 0
     1 0
     1 0
     6 0
     8 0
     1 0
    15 0
     8 0
     8 32
     8 0
     1 0
     6 0
     8 0
     8 0
     1 0

(A few important points about the above: a) The first line after the
bit that says "Resp charges for ..." refers to the net charge and total
no. of atoms respectively.
b) Each line subsequent to that refers sequentially to the atoms in
your sytem (numbered the same as in the antechamber file you begun with)
c) The left column refers to the atomic number of each atom and the
right column refers to how to treat that atom: "0" means "read in esp
charges from gaussian output file", "32" (as above) means "make this
atom equivalent in charge to atom 32."

5. The next step is to manually change the resp files so that the
removed atom will be effectively "compensated" for. In the example from
step 4 I might want to restrain atoms 22, 23, 24 and 25 because they
are to be cleaved off at a later stage. To proceed with this aim I
would add the following line to the end of BOTH the resp1 and resp2
input files (without leaving spaces!!):

     4 0.00
     1 22 1 23 1 24 1 25

The above can be interepreted as: (first line) - There are 4 atoms to
consider the sum of which must be constrained to sum to zero.
           (second line) apply this rule to moleculule 1, atom 22,
molecule 1 atom 23, molecule 1, atom 24, molecule 1, atom 25.

This would give a resp1.in file that looks like this:

Resp charges for organic molecule

  &cntrl

  nmol = 1,
  ihfree = 1,
  ioutopt = 1,

  &end
     1.0
Resp charges for organic molecule
    -1 39
     6 0
     8 0
     1 0
     1 0
     1 0
     6 0
     6 0
     6 0
     6 0
     6 0
     6 0
     7 0
     8 0
     8 0
     8 0
     1 0
     1 0
     1 0
     1 0
     1 0
     1 0
     6 0
     1 0
     1 0
     1 0
     1 0
     1 0
     6 0
     8 0
     1 0
    15 0
     8 0
     8 32
     8 0
     1 0
     6 0
     8 0
     8 0
     1 0
     4 0.00
     1 22 1 23 1 24 1 25

6. Now that you've done this edit your resp2 input file.

You should see something like this:

Resp charges for organic molecule

  &cntrl

  nmol = 1,
  ihfree = 1,
  ioutopt = 1,
  iqopt = 2,
  qwt = 0.001,

  &end
     1.0
Resp charges for organic molecule
    -1 39
     6 0 1
     8 0 2
     1 0 3
     1 0 4
     1 0 5
     6 -99 6
     6 -99 7
     6 -99 8
     6 -99 9
     6 -99 10
     6 0 11
     7 0 12
     8 -99 13
     8 -99 14
     8 -99 15
     1 -99 16
     1 -99 17
     1 -99 18
     1 -99 19
     1 0 20
     1 0 21
     6 0 22
     1 0 23
     1 0 24
     1 0 25
     1 20 26
     1 -99 27
     6 0 28
     8 0 29
     1 0 30
    15 -99 31
     8 -99 32
     8 -99 33
     8 -99 34
     1 -99 35
     6 0 36
     8 0 37
     8 0 38
     1 0 39
     4 0.00
     1 22 1 23 1 24 1 25

NB leave 4 blank lines at the end of each file or resp crashes!

The second column above is the important section. the values "-99" mean
that the charge will be varied and the value "0" means that charges
will remain the same.
At this stage all the capping groups (i.e. your hydrogen) should be set
to "0" and the remaining residues should be set to -99. In this way
each of the other Atoms is refit to "absorb" the charge of the capping
group. In the above example all atoms corresponding to the capping
groups of 22, 23, 24, 25 would be set to 0, and the remaining residies
would have their charges refitted with the "-99" flag.

7. Once you've done this then run the final leg of the resp procedure
with these commands:
        resp -i -o -t charge1 -e
        resp -i -o -q charge1 -e

8. Once you've done this you should be able to use prepgen or
antechamber to make a prep file.

9. With the prep file you can open up xleap, remove your H atom of
interest and then save the file as a library or a different prep file.

I hope that helps!

hayden

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