AMBER Archive (2009)

Subject: Re: [AMBER] tleap maximum coordination exceeded

From: Jack Shultz (js_at_drugdiscoveryathome.com)
Date: Tue Nov 17 2009 - 21:05:41 CST

It also looks like every time I do a check on this protein I get these
fata errors

> check str1
Checking 'str1'....
WARNING: The unperturbed charge of the unit: -8.000000 is not zero.
FATAL: Atom .R<NGLU 32>.A<HB1 18> does not have a type.
FATAL: Atom .R<NGLU 32>.A<HG1 19> does not have a type.
FATAL: Atom .R<NGLU 32>.A<HT2 20> does not have a type.
FATAL: Atom .R<NGLU 32>.A<HT1 21> does not have a type.
FATAL: Atom .R<LEU 33>.A<HB1 20> does not have a type.
...

On Tue, Nov 17, 2009 at 8:51 PM, Jack Shultz <js_at_drugdiscoveryathome.com> wrote:
> I'll post my pdb here
> http://boinc.drugdiscoveryathome.com/fzd8min_renum_SS.pdb
>
> Seems that this file only gives me that message when I add hydrogens
> before opening in tleap. I tried it again without adding hydrogen but
> instead I ran this command to replace residues
> # Edit Protein.pdb according to ffAMBER
> (http://chemistry.csulb.edu/ffamber/#usage)sed s/PRO\ A\ \ \ 1/NPROA\
> \ \ 1/g Protein.pdb | sed s/PRO\ B\ \ \ 1/NPROB\ \ \ 1/g \| sed s/PHE\
> A\ \ 99/CPHEA\ \ 99/g | sed s/PHE\ B\ \ 99/CPHEB\ \ 99/g \| sed s/O\ \
> \ CPHE/OC1\ CPHE/g | sed s/OXT\ CPHE/OC2\ CPHE/g \| sed s/HIS\ /HID\
> /g | sed s/LYS\ /LYP\ /g | sed s/CYS\ /CYN\ /g >| ProteinAmber.pdb
>
> str1=loadpdb ProteinAmber.pdb
>  total atoms in file: 3844
>  Leap added 494 missing atoms according to residue templates:
>       494 H / lone pairs
>  The file contained 914 atoms not in residue templates
>
> From that I was able to save the file
>
>> savepdb str1 receptor.pdb
> Writing pdb file: receptor.pdb
>  Converting N-terminal residue name to PDB format: NGLU -> GLU
>  Converting C-terminal residue name to PDB format: CARG -> ARG
>  Converting N-terminal residue name to PDB format: NGLU -> GLU
>  Converting C-terminal residue name to PDB format: CARG -> ARG
>
> but the reason I wanted to add hydrogens can be revealed in my next
> step when I try to prep it for Gromacs, which is off topic for this
> list
>
> pdb2gmx -ff amber99sb -f receptor.pdb -ignh
> I get this error message
> WARNING: atom H is missing in residue GLU 1 in the pdb file
>         You might need to add atom H to the hydrogen database of residue GLU
>         in the file ff???.hdb (see the manual)
>
> So I also tried adding hydrogens after tleap but got the same error
> message when I preped it for gromacs
> pdb2gmx -ff amber99sb -f Protein3.pdb -ignh
>
> These are the GLU 1 atoms before using babel to add H
> [boincadm_at_vps test2]$ grep "GLU     1" receptor.pdb
> ATOM      1  N   GLU     1     -20.050   8.920  -4.700  1.00  0.00
> ATOM      2  H1  GLU     1     -20.871   8.447  -5.051  1.00  0.00
> ATOM      3  H2  GLU     1     -19.241   8.579  -5.199  1.00  0.00
> ATOM      4  H3  GLU     1     -20.238   9.911  -4.660  1.00  0.00
> ATOM      5  CA  GLU     1     -19.847   8.507  -3.304  1.00  0.00
> ATOM      6  HA  GLU     1     -18.845   8.057  -3.227  1.00  0.00
> ATOM      7  CB  GLU     1     -19.913   9.782  -2.416  1.00  0.00
> ATOM      8 2HB  GLU     1     -20.026   9.493  -1.358  1.00  0.00
> ATOM      9 3HB  GLU     1     -20.055   9.447  -1.389  1.00  0.00
> ATOM     10  CG  GLU     1     -18.641  10.678  -2.498  1.00  0.00
> ATOM     11 2HG  GLU     1     -18.628  11.255  -3.435  1.00  0.00
> ATOM     12 3HG  GLU     1     -19.554  10.087  -2.431  1.00  0.00
> ATOM     13  CD  GLU     1     -18.573  11.627  -1.334  1.00  0.00
> ATOM     14  OE1 GLU     1     -19.009  12.797  -1.488  1.00  0.00
> ATOM     15  OE2 GLU     1     -18.089  11.174  -0.257  1.00  0.00
> ATOM     16  C   GLU     1     -20.807   7.451  -2.751  1.00  0.00
> ATOM     17  O   GLU     1     -21.843   7.183  -3.340  1.00  0.00
> ATOM     18 1HB  GLU     1     -20.805  10.368  -2.695  1.00  0.00
> ATOM     19 1HG  GLU     1     -17.724  10.072  -2.453  1.00  0.00
> ATOM     20 2HT  GLU     1     -19.381   9.526  -5.140  1.00  0.00
> ATOM     21 1HT  GLU     1     -20.892   8.644  -5.172  1.00  0.00
> [boincadm_at_vps test2]$
>
> These are the GLU 1 atoms after adding H
> [boincadm_at_vps test2]$ grep "GLU    32" Protein3.pdb
> ATOM      1  N   GLU    32     -20.050   8.920  -4.700  1.00  0.00           N
> ATOM      2  CA  GLU    32     -19.847   8.507  -3.304  1.00  0.00           C
> ATOM      3  C   GLU    32     -20.807   7.451  -2.751  1.00  0.00           C
> ATOM      4  O   GLU    32     -21.843   7.183  -3.340  1.00  0.00           O
> ATOM      5  CB  GLU    32     -19.913   9.782  -2.416  1.00  0.00           C
> ATOM      6  CG  GLU    32     -18.641  10.678  -2.498  1.00  0.00           C
> ATOM      7  CD  GLU    32     -18.573  11.627  -1.334  1.00  0.00           C
> ATOM      8  OE1 GLU    32     -19.009  12.797  -1.488  1.00  0.00           O
> ATOM      9  OE2 GLU    32     -18.089  11.174  -0.257  1.00  0.00           O
> ATOM     10  HA  GLU    32     -18.845   8.057  -3.227  1.00  0.00           H
> ATOM     11  HB1 GLU    32     -20.805  10.368  -2.695  1.00  0.00           H
> ATOM     12  HB2 GLU    32     -20.026   9.493  -1.358  1.00  0.00           H
> ATOM     13  HG1 GLU    32     -17.724  10.072  -2.453  1.00  0.00           H
> ATOM     14  HG2 GLU    32     -18.628  11.255  -3.435  1.00  0.00           H
> ATOM     15  HT2 GLU    32     -19.381   9.526  -5.140  1.00  0.00           H
> ATOM     16  HT1 GLU    32     -20.892   8.644  -5.172  1.00  0.00           H
> ATOM   1923  N   GLU    32      -4.048   9.370  10.471  1.00  0.00           N
> ATOM   1924  CA  GLU    32      -3.748   9.916   9.133  1.00  0.00           C
> ATOM   1925  C   GLU    32      -2.974   8.952   8.234  1.00  0.00           C
> ATOM   1926  O   GLU    32      -3.307   8.708   7.085  1.00  0.00           O
> ATOM   1927  CB  GLU    32      -2.958  11.241   9.333  1.00  0.00           C
> ATOM   1928  CG  GLU    32      -2.688  11.977   7.987  1.00  0.00           C
> ATOM   1929  CD  GLU    32      -3.954  12.422   7.305  1.00  0.00           C
> ATOM   1930  OE1 GLU    32      -4.636  13.316   7.871  1.00  0.00           O
> ATOM   1931  OE2 GLU    32      -4.261  11.878   6.212  1.00  0.00           O
> ATOM   1932  HA  GLU    32      -4.701  10.148   8.628  1.00  0.00           H
> ATOM   1933  HB1 GLU    32      -3.547  11.924   9.971  1.00  0.00           H
> ATOM   1934  HB2 GLU    32      -2.007  11.033   9.849  1.00  0.00           H
> ATOM   1935  HG1 GLU    32      -2.109  12.895   8.177  1.00  0.00           H
> ATOM   1936  HG2 GLU    32      -2.115  11.351   7.289  1.00  0.00           H
> ATOM   1937  HN2 GLU    32      -4.114   9.981  11.265  1.00  0.00           H
> ATOM   1938  HN1 GLU    32      -4.341   8.417  10.563  1.00  0.00           H
> ATOM   3845  H   GLU    32     -17.742  10.170  -0.211  1.00  0.00           H
> ATOM   3861  H   GLU    32      -5.538  13.660   7.424  1.00  0.00           H
>
>
> On Tue, Nov 17, 2009 at 3:24 PM, case <case_at_biomaps.rutgers.edu> wrote:
>> On Tue, Nov 17, 2009, Jack Shultz wrote:
>>
>>> > str1 = loadmol2 receptor2.mol2
>>> Loading Mol2 file: ./receptor2.mol2
>>> Reading MOLECULE named receptor2.mol2
>>>
>>> > savepdb str1 test.pdb
>>> savePdb: Argument #1 is type String must be of type: [unit]
>>> usage:  savePdb <object> <filename>
>>
>> This is odd.  Use the "list" command before and after the loadmol2 command to
>> see what units you have.  str1 *should* be there after (and not before).  What
>> you wrote above is supposed to work.
>>
>> ....dac
>>
>>
>> _______________________________________________
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>>
>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
> 

-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org

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