AMBER Archive (2008)

Subject: Re: AMBER: distance restraint between non-bonded molecules

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Dec 19 2008 - 09:24:09 CST

I would not recommend using center of mass restraints- we're preparing a
patch and found a bug that may goes back several versions of amber. it
doesn't always have an effect (there are several bugs, but one affects
restraints with mixing positions defined as atoms and as COM groups), but
unless you're sure you need them, don't use it until the patch is posted.

if it's still not working with 2 atoms, then you can set up a test case with
just 1 restraints and look carefully at what sander reports when reading the
restraint input (current value, distance to boundaries, etc) and also at
each time step. use that to help narrow down what sanderis doing compared to
what you want.

On Fri, Dec 19, 2008 at 10:14 AM, Taufik Al-Sarraj <
taufik.alsarraj_at_utoronto.ca> wrote:

> Hi Ilyas,
>
> Thank you for all the details. I tried what you suggested. I think AMBER
> treats this specific Nitrogen (ASN ND2) as a group. I took the RST file and
> modified the -1 to the atom number of the nitrogen only and i ran the
> simulation. I noticed that the results were very similar.
>
> Thank you again,
> Taufik
>
>
> Ilyas Yildirim wrote:
>
>> I tend not to use the scripts that come with AMBER if the system is easy
>> to create/analyze. In your case, I guess you have only 4 distance
>> restraints, is that right? If that is the case, try doing the following:
>>
>> 1. Create a .pdb file using the prmtop/inpcrd files of the simulation you
>> are intended to do. This .pdb file will order the atoms according to
>> prmtop file. This is a very crucial step!
>>
>> 2. Find which atoms are going to be restrained. For instance, for the
>> first restraint, you had :11_at_ND2 - :142_at_DT distance restrained. Find
>> those
>> atoms. You will use the corresponding atom numbers of these atoms in the
>> .pdb file while creating the RST file.
>>
>> 3. Create the lines in your RST file using the atom numbers found in step
>> # 2. As an example, look at the following entry:
>>
>> ---------------
>> # 1 RA5 1H6 14 RU3 O4 1.34 2.34
>> &rst
>> ixpk= 0, nxpk= 0, iat= 18, 431, r1= 0.84, r2= 1.34, r3= 2.34, r4=
>> 2.84,
>> rk2=25.0, rk3=25.0, ir6=1, ialtd=0,
>> &end
>> #
>> -----------------
>>
>> In this entry, the atoms of 18 and 431 (iat=18,431) are restrained. The
>> force constant used in this restraint is 25 kcal/molA^2. Check out the
>> manual to get an idea on the other parameters.
>>
>> 4. Create the other entries in the RST file, but do not include the
>> rk2,rk3,ir6,ialtd terms in the entries (the first entry has all the
>> necessary information; so you do not need to include them in the next
>> entries unless you want to change the force constants of particular
>> distance restraints).
>>
>> If you do everything right, it should work in your simulations. I am not
>> sure why you have igr1 defined in your RST entries. If only 2 atoms are
>> going to be restrained, you do not need to use igr1. It is to define a
>> group of atoms (I think). Are you planning to use distance restraints in a
>> group of atoms? In the above steps, I assumed that 2 particular atoms are
>> going to have distance restraints.
>>
>> Hope this helps. Good luck.
>>
>> On Thu, 18 Dec 2008, Taufik Al-Sarraj wrote:
>>
>>
>>
>>> Hi Ilyas,
>>> Thank you for noticing this. I did some experimenting, if i change 11
>>> ASN ND2 to something like 10 ARG CD i get
>>> # 10 ARG CD 143 DT O4 5.0 5.5
>>> &rst
>>> ixpk= 0, nxpk= 0, iat= 156,2870, r1= 4.50, r2= 5.00, r3= 5.50, r4=
>>> 6.00, &end
>>> #
>>>
>>> so the iat looks good. I looked at
>>> /usr/local/Programs/amber10.09/dat/map.DG-AMBER and i noticed that ASN
>>> ND2 has two atoms next to it. Could that be the reason?
>>>
>>> RESIDUE ASN
>>> MAPPING ND2 = HD21 HD22
>>>
>>>
>>> I also tried ASN N only and i got iat numbers that make sense
>>>
>>> Thank you,
>>> Taufik
>>>
>>> Ilyas Yildirim wrote:
>>>
>>>
>>>> the RST file is
>>>>> #
>>>>> # 11 ASN ND2 142 DT O4 2.5
>>>>> &rst
>>>>> ixpk= 0, nxpk= 0, iat= -1,2838, r1= 1.30, r2= 1.80, r3= 2.81, r4=
>>>>> 3.31,
>>>>>
>>>>> rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
>>>>> igr1= 180, 181,
>>>>> &end
>>>>> #
>>>>> # 11 ASN ND2 143 DT O4 5.5
>>>>> &rst
>>>>> ixpk= 0, nxpk= 0, iat= -1,2870, r1= 1.30, r2= 1.80, r3= 6.17, r4=
>>>>> 6.67,
>>>>> igr1= 180, 181,
>>>>> &end
>>>>> #
>>>>> # 69 ASN ND2 121 DT O4 2.5
>>>>> &rst
>>>>> ixpk= 0, nxpk= 0, iat= -1,2171, r1= 1.30, r2= 1.80, r3= 2.81, r4=
>>>>> 3.31,
>>>>> igr1=1179,1180,
>>>>> &end
>>>>> #
>>>>> # 69 ASN ND2 122 DT O4 5.5
>>>>> &rst
>>>>> ixpk= 0, nxpk= 0, iat= -1,2203, r1= 1.30, r2= 1.80, r3= 6.17, r4=
>>>>> 6.67,
>>>>> igr1=1179,1180,
>>>>> &end
>>>>>
>>>>>
>>>>>
>>>> The atoms that are restrained in the first case are atom number -1 and
>>>> and
>>>> atom number 2838. This does not look so normal. It should be a positive
>>>> number. Generally I re-create the .pdb using the prmtop/inpcrd files,
>>>> and
>>>> then use that .pdb file to create the RST file.
>>>>
>>>>
>>>>
>>>>
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>>>
>>>
>>
>>
>>
>
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