AMBER Archive (2009)

Subject: Re: [AMBER] tleap maximum coordination exceeded

From: Jack Shultz (js_at_drugdiscoveryathome.com)
Date: Tue Nov 17 2009 - 19:51:38 CST

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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Jack

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

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