AMBER Archive (2009)

Subject: [AMBER] RE: AMBER: xleap problem

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jan 06 2009 - 21:58:26 CST

Hi Bala,

 

It's not clear what is going on here - can you post the actual pdb file?

 

Is it possible that there is duplication between the two chains that you
have?

 

I thought it might be a problem with spacing but comparing one of your lines
with that from a kosha pdb file it looks okay:

 

ATOM 744 N VAL G 245 86.769-152.726 108.476 1.00142.71 N

 

ATOM 34 N VAL 3 -0.432 25.796 25.423 1.00 8.21 1PLC
157

 

You could try removing the column between the residue name and the residue
ID. I.e. remove ' G '.

 

Something like:

 

sed 's/ G / /' my.pdb > my2.pdb

 

will probably do it although you may have to check for false positives. You
could also use emacs to yank out the column and replace the G with a space.

 

There may be some other subtle problem with your pdb file though and it
would help to be able to see the pdb file itself.

 

All the best

Ross

 

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Bala subramanian
Sent: Tuesday, January 06, 2009 11:43 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: xleap problem

 

This is a pdb of a complex that constitutes of two proteins. The individual
chains are seperated by TER card

On Tue, Jan 6, 2009 at 8:05 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:

are you sure that is the only thing in the pdb file? (not more than 1
model, etc)

On Tue, Jan 6, 2009 at 1:57 PM, Bala subramanian
<bala.biophysics_at_gmail.com> wrote:
> Dear users,
>
> When i load a pdb in xleap. I get the following message. But the atom
names
> in my pdb files especially for these residues are indeed unique. Kindly
> write me what is going wrong. I am using amber9 and using ff99SB
forcefield.
>
>> b = loadPDB "/home/bala/ggp/ggp_b.pdb"
> Loading PDB file: /home/bala/ggp/ggp_b.pdb
> Enter zPdbReadScan from call depth 0.
> -- residue 246: duplicate [ C] atoms (total 2)
> -- residue 246: duplicate [ CA] atoms (total 2)
> -- residue 246: duplicate [ N] atoms (total 2)
> -- residue 246: duplicate [ O] atoms (total 2)
> -- residue 247: duplicate [ C] atoms (total 2)
> -- residue 247: duplicate [ CA] atoms (total 2)
> -- residue 247: duplicate [ CB] atoms (total 2)
> -- residue 247: duplicate [ CD] atoms (total 2)
> -- residue 247: duplicate [ CG] atoms (total 2)
> -- residue 247: duplicate [ N] atoms (total 2)
> -- residue 247: duplicate [ O] atoms (total 2)
> -- residue 248: duplicate [ C] atoms (total 2)
> -- residue 248: duplicate [ CA] atoms (total 2)
> -- residue 248: duplicate [ N] atoms (total 2)
> -- residue 248: duplicate [ O] atoms (total 2)
>
> ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
> (same-name atoms are reduced to a single atom)
>
>
> The following is the portion from the pdb for these residues
> ATOM 744 N VAL G 245 86.769-152.726 108.476 1.00142.71
> N
> ATOM 745 CA VAL G 245 86.005-153.338 109.549 1.00143.44
> C
> ATOM 746 C VAL G 245 84.747-152.503 109.763 1.00143.75
> C
> ATOM 747 O VAL G 245 84.627-151.413 109.204 1.00143.15
> O
> ATOM 748 CB VAL G 245 86.821-153.377 110.853 1.00144.12
> C
> ATOM 749 CG1 VAL G 245 87.881-154.460 110.778 1.00144.77
> C
> ATOM 750 CG2 VAL G 245 87.479-152.032 111.086 1.00144.53
> C
> ATOM 751 N GLN G 246 83.808-153.006 110.557 1.00144.36
> N
> ATOM 752 CA GLN G 246 82.577-152.266 110.799 1.00144.77
> C
> ATOM 753 C GLN G 246 82.652-151.364 112.024 1.00144.15
> C
> ATOM 754 O GLN G 246 82.087-150.272 112.025 1.00143.24
> O
> ATOM 755 CB GLN G 246 81.392-153.227 110.918 1.00146.20
> C
> ATOM 756 CG GLN G 246 81.220-154.117 109.699 1.00148.95
> C
> ATOM 757 CD GLN G 246 81.195-153.327 108.400 1.00150.00
> C
> ATOM 758 OE1 GLN G 246 80.344-152.461 108.202 1.00150.67
> O
> ATOM 759 NE2 GLN G 246 82.136-153.623 107.510 1.00149.89
> N
> ATOM 760 N CYX G 247 83.338-151.814 113.069 1.00143.81
> N
> ATOM 761 CA CYX G 247 83.474-150.999 114.274 1.00143.17
> C
> ATOM 762 C CYX G 247 84.949-150.785 114.595 1.00142.65
> C
> ATOM 763 O CYX G 247 85.796-151.613 114.255 1.00142.71
> O
> ATOM 764 CB CYX G 247 82.810-151.662 115.485 1.00142.99
> C
> ATOM 765 SG CYX G 247 80.988-151.740 115.542 1.00143.43
> S
> ATOM 766 N THR G 248 85.247-149.676 115.262 1.00141.73
> N
> ATOM 767 CA THR G 248 86.613-149.336 115.640 1.00140.76
> C
> ATOM 768 C THR G 248 87.070-150.095 116.883 1.00140.31
> C
> ATOM 769 O THR G 248 86.258-150.456 117.731 1.00140.20
> O
> ATOM 770 CB THR G 248 86.725-147.838 115.923 1.00140.39
> C
> ATOM 771 OG1 THR G 248 86.168-147.112 114.824 1.00141.14
> O
> ATOM 772 CG2 THR G 248 88.169-147.433 116.094 1.00140.10
> C
> ATOM 773 N HIS G 249 88.375-150.325 116.991 1.00139.86
> N
> ATOM 774 CA HIS G 249 88.932-151.035 118.138 1.00139.38
> C
> ATOM 775 C HIS G 249 88.597-150.355 119.464 1.00137.88
> C
> ATOM 776 O HIS G 249 88.282-149.167 119.501 1.00138.46
> O
> ATOM 777 CB HIS G 249 90.449-151.170 117.990 1.00140.83
> C
> ATOM 778 CG HIS G 249 90.872-152.257 117.049 1.00143.17
> C
> ATOM 779 ND1 HIS G 249 90.448-152.316 115.739 1.00143.35
> N
> ATOM 780 CD2 HIS G 249 91.689-153.323 117.227 1.00143.40
> C
> ATOM 781 CE1 HIS G 249 90.986-153.371 115.151 1.00143.13
> C
> ATOM 782 NE2 HIS G 249 91.743-153.998 116.032 1.00143.09
> N
>
>
> Thank you,
> Bala
>
>
>

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