Re: AMBER: problems in adding ACE and NME group

From: Melinda Layten <mlayten.gmail.com>
Date: Wed, 27 Jun 2007 12:01:00 -0400

Read your error carefully. ACE needs to be the first line of your pdb file
and you need to delete atom H1. Right now, you are creating NALA (1) and
then ACE (2) and that's what's causing your problems

On 6/27/07, backy <backy.ibms.sinica.edu.tw> wrote:
>
> Hi, amber users:
>
> Based on Melinda's suggestion, the pdb file was modified like this below.
> But the *.top file was still not available.
>
> :(
>
>
>
> backy
>
>
>
>
>
> REMARK
> ATOM 1 N ALA 1 70.146 65.827 40.009
> ATOM 2 H1 ALA 1 69.336 66.290 40.398
> ATOM 3 C ACE 1 70.907 65.903 40.670
> ATOM 4 H3 ALA 1 69.929 64.849 39.886
> ATOM 5 CA ALA 1 70.526 66.443 38.710
> ATOM 6 HA ALA 1 71.550 66.812 38.798
> ATOM 7 CB ALA 1 70.498 65.414 37.563
> .
> .
> .
>
> ATOM 2327 NE2 HID 149 72.425 63.869 32.001
> ATOM 2328 CD2 HID 149 72.081 64.901 32.885
> ATOM 2329 HD2 HID 149 72.158 64.871 33.964
> ATOM 2330 C HID 149 73.678 68.044 32.727
> ATOM 2331 O HID 149 74.527 67.959 31.808
> ATOM 2332 N NME 149 73.966 67.822 33.927
> TER
> END
>
>
>
>
>
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: ./leapin
> ----- Source: /home/.2/amber9/dat/leap/cmd/leaprc.ff03
> ----- Source of /home/.2/amber9/dat/leap/cmd/leaprc.ff03 done
> Log file: ./leap.log
> Loading parameters: /home/.2/amber9/dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02
> /04/99
> Loading parameters: /home/.2/amber9/dat/leap/parm/frcmod.ff03
> Reading force field modification type file (frcmod)
> Reading title:
> Duan et al ff03 phi psi torsions
> Loading library: /home/.2/amber9/dat/leap/lib/ions94.lib
> Loading library: /home/.2/amber9/dat/leap/lib/solvents.lib
> Loading library: /home/.2/amber9/dat/leap/lib/all_nucleic94.lib
> Loading library: /home/.2/amber9/dat/leap/lib/all_aminoct94.lib
> Loading library: /home/.2/amber9/dat/leap/lib/all_aminont94.lib
> Loading library: /home/.2/amber9/dat/leap/lib/all_amino03.lib
> Using Bondi radii
> Loading PDB file: ./1jbs-A-wild.pdb
> Warning: name change in pdb file residue 1 ;
> this residue is split into ALA and ACE.
> Warning: name change in pdb file residue 1 ;
> this residue is split into ACE and ALA.
> Warning: name change in pdb file residue 149 ;
> this residue is split into HID and NME.
> 3 residues had naming warnings.
> There are split residues;
> residue sequence numbers will not correspond to those in the pdb.
> Added missing heavy atom: .R<NALA 1>.A<CA 5>
> Added missing heavy atom: .R<NALA 1>.A<CB 7>
> Added missing heavy atom: .R<NALA 1>.A<C 11>
> Added missing heavy atom: .R<NALA 1>.A<O 12>
> Bond: Maximum coordination exceeded on .R<ACE 2>.A<HH31 1>
> -- setting atoms pert=true overrides default limits
> Added missing heavy atom: .R<ACE 2>.A<CH3 2>
> Added missing heavy atom: .R<ACE 2>.A<O 6>
> Created a new atom named: H3 within residue: .R<ALA 3>
> Added missing heavy atom: .R<ALA 3>.A<N 1>
> Added missing heavy atom: .R<NME 152>.A<CH3 3>
> total atoms in file: 2332
> Leap added 22 missing atoms according to residue templates:
> 8 Heavy
> 14 H / lone pairs
> The file contained 1 atoms not in residue templates
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 11.000000 is not zero.
> FATAL: Atom .R<ALA 3>.A<H3 11> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Quit
>
>
>
>
>
> ----- Original Message -----
> *From:* Melinda Layten <mlayten.gmail.com>
> *To:* amber.scripps.edu
> *Sent:* Wednesday, June 27, 2007 4:02 AM
> *Subject:* Re: AMBER: problems in adding ACE and NME group
>
>
> You can also run leap with your normal 1-149 no capping groups, save the
> pdb file and in the new pdb rename H2 of res 1 to C of ACE and OXT of 149 to
> N of NME.
>
> Once leap runs correctly and you can visualize your molecule in VMD or
> similar, then start worrying about running sander.
>
> Melinda
>
> On 6/25/07, priya priya <priyaanand_27.yahoo.co.in> wrote:
> >
> > you can use xleap to add ACE and NME to cap the system
> >
> > *backy < backy.ibms.sinica.edu.tw>* wrote:
> >
> > Actually, how users cap the protein terminal?
> > For example, by which kind of program to put the initial coordinates for
> > ACE
> > and NME groups?
> >
> > backy
> > ----- Original Message -----
> > From: "David A. Case"
> > To:
> > Sent: Thursday, June 21, 2007 1:10 PM
> > Subject: Re: AMBER: problems in adding ACE and NME group
> >
> >
> > > On Thu, Jun 21, 2007, backy wrote:
> > >
> > >> If there is a need in placing the whole ACE and NME group, how should
> > I
> > >> input their initial coordinations?
> > >
> > > This is a very rare thing to do, and Amber admitedly doesn't make it
> > very
> > > easy. It isn't something I would recommend just "for practice".
> > >
> > > You might use a homology-modeling program to add alanine at both ends,
> >
> > > then
> > > delete the atoms you don't need, and change the residue names to ACE
> > and
> > > NME.
> > >
> > > ....dac
> > >
> > >
> > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber.scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > >
> > >
> > >
> > > --
> > > No virus found in this incoming message.
> > > Checked by AVG Free Edition.
> > > Version: 7.5.472 / Virus Database: 269.9.1/857 - Release Date:
> > 2007/6/20
> > > U 02:18
> > >
> > >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
> >
> > ------------------------------
> > Did you know? You can CHAT without downloading messenger. Click here<http://in.rd.yahoo.com/tagline_webmessenger_2/*http://in.messenger.yahoo.com/webmessengerpromo.php>
> >
> >
> ------------------------------
>
> No virus found in this incoming message.
> Checked by AVG Free Edition.
> Version: 7.5.476 / Virus Database: 269.9.9/872 - Release Date: 2007/6/26
> $U$H 06:43
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jul 01 2007 - 06:07:09 PDT
Custom Search