AMBER Archive (2009)

Subject: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Nov 04 2009 - 07:39:02 CST

Dear Zhou Gong,

The information reported here:
http://archive.ambermd.org/200910/0191.html
might be helful to understand what is a force field library, how to
use it and when one needs to create a new one.

regards, Francois

> Dear sir
> Could you please tell me in detail how can I create a unit
> that just has these atoms ?
> I have change the name of ADE to "SOL", however, the errors still exsit
>
> PDB file:
>
> ATOM 1493 C6 G X 83 3.005 3.061 -0.159 1.00 89.27
> C
> ATOM 1494 O6 G X 83 2.942 2.890 1.064 1.00 89.30
> O
> ATOM 1495 N1 G X 83 2.590 2.068 -1.054 1.00 89.82
> N
> ATOM 1496 C2 G X 83 2.629 2.186 -2.432 1.00 89.50
> C
> ATOM 1497 N2 G X 83 2.185 1.128 -3.130 1.00 89.30
> N
> ATOM 1498 N3 G X 83 3.069 3.273 -3.071 1.00 89.41
> N
> ATOM 1499 C4 G X 83 3.479 4.245 -2.208 1.00 89.41
> C
> TER 1500 G X 83
>
> HETATM 1506 N9 SOL X 90 18.599 -19.496 5.363 1.00 36.40
> N
> HETATM 1507 C8 SOL X 90 19.317 -18.826 6.330 1.00 37.43
> C
> HETATM 1508 N7 SOL X 90 19.960 -17.765 5.878 1.00 37.14
> N
> HETATM 1509 C5 SOL X 90 19.606 -17.738 4.549 1.00 37.42
> C
> HETATM 1510 C6 SOL X 90 19.944 -16.854 3.520 1.00 37.76
> C
> HETATM 1511 N6 SOL X 90 20.739 -15.818 3.734 1.00 36.15
> N
> HETATM 1512 N1 SOL X 90 19.447 -17.084 2.287 1.00 36.86
> N
> HETATM 1513 C2 SOL X 90 18.651 -18.139 2.096 1.00 37.35
> C
> HETATM 1514 N3 SOL X 90 18.270 -19.058 2.981 1.00 38.33
> N
> HETATM 1515 C4 SOL X 90 18.784 -18.792 4.203 1.00 37.55
> C
>
> tleap output
>
>> model=loadpdb 1y26_a.pdb
> Loading PDB file: ./1y26_a.pdb
> Unknown residue: SOL number: 71 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: SOL sequence: 84
> Created a new atom named: N9 within residue: .R<SOL 84>
> Created a new atom named: C8 within residue: .R<SOL 84>
> Created a new atom named: N7 within residue: .R<SOL 84>
> Created a new atom named: C5 within residue: .R<SOL 84>
> Created a new atom named: C6 within residue: .R<SOL 84>
> Created a new atom named: N6 within residue: .R<SOL 84>
> Created a new atom named: N1 within residue: .R<SOL 84>
> Created a new atom named: C2 within residue: .R<SOL 84>
> Created a new atom named: N3 within residue: .R<SOL 84>
> Created a new atom named: C4 within residue: .R<SOL 84>
> total atoms in file: 1509
> Leap added 758 missing atoms according to residue templates:
> 758 H / lone pairs
> The file contained 10 atoms not in residue templates
>
> Thank you very much
>
>
> 2009-11-04
>
>
>
> Zhou Gong
> School of Physics
> Huazhong University of Science and Technology
> Wuhan
> Hubei Province
> China
>
>
>
> 发件人： case
> 发送时间： 2009-11-04 20:19:30
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: [AMBER] errors on leap for a RNA+Adenine pdb structure
>
> On Wed, Nov 04, 2009, zgong.hust wrote:
>>
>> I would like to simulate the RNA with one seperate Adenine
>> molecule. The end of the PDB file is like this
>>
> ....
>> ATOM 1496 C2 G X 83 2.629 2.186 -2.432 1.00 89.50
>> C
>> ATOM 1497 N2 G X 83 2.185 1.128 -3.130 1.00 89.30
>> N
>> ATOM 1498 N3 G X 83 3.069 3.273 -3.071 1.00 89.41
>> N
>> ATOM 1499 C4 G X 83 3.479 4.245 -2.208 1.00 89.41
>> C
>> TER 1500 G X 83
>> HETATM 1506 N9 ADE X 90 18.599 -19.496 5.363 1.00 36.40
>> N
>> HETATM 1507 C8 ADE X 90 19.317 -18.826 6.330 1.00 37.43
>> C
>> HETATM 1508 N7 ADE X 90 19.960 -17.765 5.878 1.00 37.14
>> N
>> HETATM 1509 C5 ADE X 90 19.606 -17.738 4.549 1.00 37.42
>> C
>> HETATM 1510 C6 ADE X 90 19.944 -16.854 3.520 1.00 37.76
>> C
>> HETATM 1511 N6 ADE X 90 20.739 -15.818 3.734 1.00 36.15
>> N
>> HETATM 1512 N1 ADE X 90 19.447 -17.084 2.287 1.00 36.86
>> N
>> HETATM 1513 C2 ADE X 90 18.651 -18.139 2.096 1.00 37.35
>> C
>> HETATM 1514 N3 ADE X 90 18.270 -19.058 2.981 1.00 38.33
>> N
>> HETATM 1515 C4 ADE X 90 18.784 -18.792 4.203 1.00 37.55
>> C
>>
>> There are ten Adenine atoms at the end of the pdb file
>>
>> When I use the tleap with leap.rna.ff98 force field, some errors happened
>>
>> > model=loadpdb 1y26_1.pdb
>> Loading PDB file: ./1y26_1.pdb
>> Added missing heavy atom: .R<RA3 84>.A<C1' 11>
>> Added missing heavy atom: .R<RA3 84>.A<O4' 10>
> In the Amber library, "ADE" means adenosine (the nucleotide), not just the
> base. It's probably easiest to rename the ADE part to something else, and to
> create a unit that just has those atoms.
> ...dac

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