RE: AMBER: problems in adding ACE and NME group

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 27 Jun 2007 09:02:10 -0700

Hi Backy
 
Try doing this:
 
ATOM 1 C ACE 1 70.907 65.903 40.670
ATOM 1 N ALA 2 70.146 65.827 40.009
ATOM 2 H1 ALA 2 69.336 66.290 40.398
ATOM 4 H3 ALA 2 69.929 64.849 39.886
ATOM 5 CA ALA 2 70.526 66.443 38.710
ATOM 6 HA ALA 2 71.550 66.812 38.798
ATOM 7 CB ALA 2 70.498 65.414 37.563

.
.
.

ATOM 2327 NE2 HID 150 72.425 63.869 32.001
ATOM 2328 CD2 HID 150 72.081 64.901 32.885
ATOM 2329 HD2 HID 150 72.158 64.871 33.964
ATOM 2330 C HID 150 73.678 68.044 32.727
ATOM 2331 O HID 150 74.527 67.959 31.808
ATOM 2332 N NME 151 73.966 67.822 33.927
TER
END

 

Note the renumbering of the residues - you'll likely have to script this -
awk is good for this sort of thing.

 

Then when you load this into leap it should add missing atoms only for the
ACE and NME. Then select those two residues in leap and relax the selection
- I.e. relax the ACE and NME residues since they will have very bad initial
geometries. Then you should be able to create your prmtop and inpcrd files -
and hopefully be able to stably minimize - if you run into problems at the
minimization stage you may need to restrain everything except the ACE and
NME for the first stage of minimization.

 

I haven't been following this thread so this question may have already been
asked but why do you want to cap you entire protein with ACE and NME? Can
you not just leave it as the ion?

 

Normally you only cap with ACE and NME when you are trying to derive charges
for a new residue - say an modified amino acid. e.g. say you had modified
glutamine (call GLX), and you needed to calculate RESP charges. You would
build ACE-GLX-NME. Do a gas phase HF/6-31G* calculation (for FF99xx) to get
the ESP. Then you put this into RESP and do the resp fit keeping the ACE and
NME charges fixed at their published values. I can't see why you would want
to cap and entire protein chain.

 

All the best

Ross

 

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

 



  _____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
backy
Sent: Tuesday, June 26, 2007 23:56
To: amber.scripps.edu
Subject: Re: AMBER: problems in adding ACE and NME group



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 <mailto:mlayten.gmail.com> Layten
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 < <mailto:backy.ibms.sinica.edu.tw> 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.co
m/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