AMBER Archive (2008)

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

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Fri Dec 19 2008 - 09:14:51 CST

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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