AMBER Archive (2008)

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

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Thu Dec 18 2008 - 14:41:05 CST

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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