subject:"\[gmx\-users\] Fatal error\: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms"

Re: [gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms

2009-11-04 Thread Justin A. Lemkul




Chandan Choudhury wrote:

My complete input file is

ATOM  1 NCCMT   1  -2.521  -2.813   2.083  0.00  0.00
ATOM  2 CA   CCMT   1  -2.925  -1.739   1.166  0.00  0.00
ATOM  3 CCCMT   1  -1.711  -0.842   0.859  0.00  0.00
ATOM  4 CB   CCMT   1  -4.034  -0.895   1.821  0.00  0.00
ATOM  5 SG   CCMT   1  -4.523   0.408   0.710  0.00  0.00
ATOM  6 SD   CCMT   1  -5.981   1.512   1.567  0.00  0.00
ATOM  7 CE   CCMT   1  -7.394   0.480   1.895  0.00  0.00
ATOM  8 CZ   CCMT   1  -6.988  -0.662   2.846  0.00  0.00
ATOM  9 CH   CCMT   1  -7.604  -2.072   2.895  0.00  0.00
ATOM 10 CH1  CCMT   1  -8.797  -2.090   3.869  0.00  0.00
ATOM 11 CH2  CCMT   1  -8.096  -2.574   1.525  0.00  0.00
ATOM 12 CI   CCMT   1  -5.986  -1.995   4.476  0.00  0.00
ATOM 13 CI1  CCMT   1  -4.582  -2.406   4.958  0.00  0.00
ATOM 14 CI2  CCMT   1  -6.931  -2.001   5.692  0.00  0.00
ATOM 15 CK   CCMT   1  -6.018  -0.615   3.792  0.00  0.00
ATOM 16 NT1  CCMT   1  -6.486  -2.876   3.411  0.00  0.00
ATOM 17 OC1  CCMT   1  -0.511  -1.346   0.867  0.00  0.00
ATOM 18 OC2  CCMT   1  -1.885   0.420   0.592  0.00  0.00
ATOM 19 OT1  CCMT   1  -6.836  -4.122   3.830  0.00  0.00
ATOM 20 HCCMT   1  -1.801  -3.362   1.658  0.00  0.00
ATOM 21 HA   CCMT   1  -3.292  -2.165   0.256  0.00  0.00
ATOM 22 HB1  CCMT   1  -4.878  -1.518   2.033  0.00  0.00
ATOM 23 HB2  CCMT   1  -3.668  -0.468   2.731  0.00  0.00
ATOM 24 HE1  CCMT   1  -7.754   0.067   0.976  0.00  0.00
ATOM 25 HE2  CCMT   1  -8.165   1.065   2.350  0.00  0.00
ATOM 26 HH11 CCMT   1  -9.175  -3.088   3.952  0.00  0.00
ATOM 27 HH21 CCMT   1  -8.875  -1.932   1.170  0.00  0.00
ATOM 28 HH12 CCMT   1  -8.477  -1.749   4.832  0.00  0.00
ATOM 29 HH22 CCMT   1  -7.283  -2.566   0.829  0.00  0.00
ATOM 30 HH13 CCMT   1  -9.567  -1.446   3.500  0.00  0.00
ATOM 31 HH23 CCMT   1  -8.471  -3.571   1.624  0.00  0.00
ATOM 32 HI11 CCMT   1  -4.241  -1.712   5.697  0.00  0.00
ATOM 33 HI21 CCMT   1  -6.956  -2.982   6.119  0.00  0.00
ATOM 34 HI12 CCMT   1  -4.624  -3.387   5.383  0.00  0.00
ATOM 35 HI22 CCMT   1  -6.577  -1.303   6.422  0.00  0.00
ATOM 36 HI13 CCMT   1  -3.906  -2.405   4.128  0.00  0.00
ATOM 37 HI23 CCMT   1  -7.915  -1.722   5.380  0.00  0.00
ATOM 38 HK   CCMT   1  -5.391   0.221   4.019  0.00  0.00
ATOM 39 NNARG   2  -4.657  -5.920   2.257  0.00  0.00
ATOM 40 CA   NARG   2  -3.476  -5.161   2.694  0.00  0.00
ATOM 41 CNARG   2  -3.680  -3.668   2.378  0.00  0.00
ATOM 42 ONARG   2  -4.839  -3.179   2.371  0.00  0.00
ATOM 43 CB   NARG   2  -2.230  -5.679   1.952  0.00  0.00
ATOM 44 CG   NARG   2  -0.992  -4.885   2.410  0.00  0.00
ATOM 45 CZ   NARG   2   2.459  -4.459   1.265  0.00  0.00
ATOM 46 CD   NARG   2   0.254  -5.404   1.668  0.00  0.00
ATOM 47 NE   NARG   2   1.436  -4.648   2.106  0.00  0.00
ATOM 48 NH1  NARG   2   2.406  -4.958   0.025  0.00  0.00
ATOM 49 NH2  NARG   2   3.535  -3.771   1.664  0.00  0.00
ATOM 50 HA   NARG   2  -3.341  -5.287   3.748  0.00  0.00
ATOM 51 HB1  NARG   2  -2.089  -6.716   2.172  0.00  0.00
ATOM 52 HB2  NARG   2  -2.365  -5.552   0.898  0.00  0.00
ATOM 53 HG1  NARG   2  -1.132  -3.847   2.190  0.00  0.00
ATOM 54 HG2  NARG   2  -0.858  -5.011   3.464  0.00  0.00
ATOM 55 HD1  NARG   2   0.393  -6.442   1.888  0.00  0.00
ATOM 56 HD2  NARG   2   0.120  -5.278   0.614  0.00  0.00
ATOM 57 HE   NARG   2   1.475  -4.274   3.033  0.00  0.00
ATOM 58 HH11 NARG   2   1.602  -5.472  -0.274  0.00  0.00
ATOM 59 HH21 NARG   2   3.574  -3.398   2.591  0.00  0.00
ATOM 60 HH12 NARG   2   3.171  -4.817  -0.604  0.00  0.00
ATOM 61 HH22 NARG   2   4.299  -3.631   1.035  0.00  0.00
ATOM 62 H1   NARG   2  -5.466  -5.584   2.740  0.00  0.00
ATOM 63 H2   NARG   2  -4.525  -6.890   2.463  0.00  0.00
ATOM 64 H3   NARG   2  -4.783  -5.802   1.272  0.00  0.00
END




Is your goal a dipeptide of NARG-CCMT?  If so, think about the order.  If CCMT 
comes first, pdb2gmx is going to try to make an amide bond between the 
carboxylate of CCMT and the amino group of NARG, deleting and replacing whatever 
it has to.  Does your CCMT .rtp entry define any bonds, or is it just the atom 
entries you showed before?


I would suggest putting the amino acids in the proper order (N-terminal first) 
and see if that fixes the problem.


-Justin



On Wed, Nov 4, 2009 at 7:54 AM, Mark Abraham > wrote:


Chandan Choudhury wrote:

Hi everyone !!

I am having  a problem using pdb2gmx command. Using the command
on my input pdb fi

Re: [gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms

2009-11-03 Thread Mark Abraham


Chandan Choudhury wrote:

My complete input file is

ATOM  1 NCCMT   1  -2.521  -2.813   2.083  0.00  0.00
ATOM  2 CA   CCMT   1  -2.925  -1.739   1.166  0.00  0.00
ATOM  3 CCCMT   1  -1.711  -0.842   0.859  0.00  0.00
ATOM  4 CB   CCMT   1  -4.034  -0.895   1.821  0.00  0.00
ATOM  5 SG   CCMT   1  -4.523   0.408   0.710  0.00  0.00
ATOM  6 SD   CCMT   1  -5.981   1.512   1.567  0.00  0.00
ATOM  7 CE   CCMT   1  -7.394   0.480   1.895  0.00  0.00
ATOM  8 CZ   CCMT   1  -6.988  -0.662   2.846  0.00  0.00
ATOM  9 CH   CCMT   1  -7.604  -2.072   2.895  0.00  0.00
ATOM 10 CH1  CCMT   1  -8.797  -2.090   3.869  0.00  0.00
ATOM 11 CH2  CCMT   1  -8.096  -2.574   1.525  0.00  0.00
ATOM 12 CI   CCMT   1  -5.986  -1.995   4.476  0.00  0.00
ATOM 13 CI1  CCMT   1  -4.582  -2.406   4.958  0.00  0.00
ATOM 14 CI2  CCMT   1  -6.931  -2.001   5.692  0.00  0.00
ATOM 15 CK   CCMT   1  -6.018  -0.615   3.792  0.00  0.00
ATOM 16 NT1  CCMT   1  -6.486  -2.876   3.411  0.00  0.00
ATOM 17 OC1  CCMT   1  -0.511  -1.346   0.867  0.00  0.00
ATOM 18 OC2  CCMT   1  -1.885   0.420   0.592  0.00  0.00
ATOM 19 OT1  CCMT   1  -6.836  -4.122   3.830  0.00  0.00
ATOM 20 HCCMT   1  -1.801  -3.362   1.658  0.00  0.00
ATOM 21 HA   CCMT   1  -3.292  -2.165   0.256  0.00  0.00
ATOM 22 HB1  CCMT   1  -4.878  -1.518   2.033  0.00  0.00
ATOM 23 HB2  CCMT   1  -3.668  -0.468   2.731  0.00  0.00
ATOM 24 HE1  CCMT   1  -7.754   0.067   0.976  0.00  0.00
ATOM 25 HE2  CCMT   1  -8.165   1.065   2.350  0.00  0.00
ATOM 26 HH11 CCMT   1  -9.175  -3.088   3.952  0.00  0.00
ATOM 27 HH21 CCMT   1  -8.875  -1.932   1.170  0.00  0.00
ATOM 28 HH12 CCMT   1  -8.477  -1.749   4.832  0.00  0.00
ATOM 29 HH22 CCMT   1  -7.283  -2.566   0.829  0.00  0.00
ATOM 30 HH13 CCMT   1  -9.567  -1.446   3.500  0.00  0.00
ATOM 31 HH23 CCMT   1  -8.471  -3.571   1.624  0.00  0.00
ATOM 32 HI11 CCMT   1  -4.241  -1.712   5.697  0.00  0.00
ATOM 33 HI21 CCMT   1  -6.956  -2.982   6.119  0.00  0.00
ATOM 34 HI12 CCMT   1  -4.624  -3.387   5.383  0.00  0.00
ATOM 35 HI22 CCMT   1  -6.577  -1.303   6.422  0.00  0.00
ATOM 36 HI13 CCMT   1  -3.906  -2.405   4.128  0.00  0.00
ATOM 37 HI23 CCMT   1  -7.915  -1.722   5.380  0.00  0.00
ATOM 38 HK   CCMT   1  -5.391   0.221   4.019  0.00  0.00
ATOM 39 NNARG   2  -4.657  -5.920   2.257  0.00  0.00
ATOM 40 CA   NARG   2  -3.476  -5.161   2.694  0.00  0.00
ATOM 41 CNARG   2  -3.680  -3.668   2.378  0.00  0.00
ATOM 42 ONARG   2  -4.839  -3.179   2.371  0.00  0.00
ATOM 43 CB   NARG   2  -2.230  -5.679   1.952  0.00  0.00
ATOM 44 CG   NARG   2  -0.992  -4.885   2.410  0.00  0.00
ATOM 45 CZ   NARG   2   2.459  -4.459   1.265  0.00  0.00
ATOM 46 CD   NARG   2   0.254  -5.404   1.668  0.00  0.00
ATOM 47 NE   NARG   2   1.436  -4.648   2.106  0.00  0.00
ATOM 48 NH1  NARG   2   2.406  -4.958   0.025  0.00  0.00
ATOM 49 NH2  NARG   2   3.535  -3.771   1.664  0.00  0.00
ATOM 50 HA   NARG   2  -3.341  -5.287   3.748  0.00  0.00
ATOM 51 HB1  NARG   2  -2.089  -6.716   2.172  0.00  0.00
ATOM 52 HB2  NARG   2  -2.365  -5.552   0.898  0.00  0.00
ATOM 53 HG1  NARG   2  -1.132  -3.847   2.190  0.00  0.00
ATOM 54 HG2  NARG   2  -0.858  -5.011   3.464  0.00  0.00
ATOM 55 HD1  NARG   2   0.393  -6.442   1.888  0.00  0.00
ATOM 56 HD2  NARG   2   0.120  -5.278   0.614  0.00  0.00
ATOM 57 HE   NARG   2   1.475  -4.274   3.033  0.00  0.00
ATOM 58 HH11 NARG   2   1.602  -5.472  -0.274  0.00  0.00
ATOM 59 HH21 NARG   2   3.574  -3.398   2.591  0.00  0.00
ATOM 60 HH12 NARG   2   3.171  -4.817  -0.604  0.00  0.00
ATOM 61 HH22 NARG   2   4.299  -3.631   1.035  0.00  0.00
ATOM 62 H1   NARG   2  -5.466  -5.584   2.740  0.00  0.00
ATOM 63 H2   NARG   2  -4.525  -6.890   2.463  0.00  0.00
ATOM 64 H3   NARG   2  -4.783  -5.802   1.272  0.00  0.00
END


This looks like you are trying to convert a non-covalently-bound ligand 
and an ARG-terminated protein in the same structure. If you'd described 
what you were trying to do in words in your first post, that would have 
been helpful. Your approach might work if you use PDB chain identifiers 
properly.


Also possible is to run pdb2gmx on isolated ligand, and separately on 
isolated protein. Edit the two top files to convert them to .itp files, 
and #include them in a new master .top file. This might be a good idea 
for some workflows. See 
http://www.gromacs.org/Documentation/File_Formats/.top_File and links 
from it.


Mark

On Wed, Nov 4, 2009 at 7:54 AM, Mark Abraham > wro

Re: [gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms

2009-11-03 Thread Chandan Choudhury

My complete input file is

ATOM  1 NCCMT   1  -2.521  -2.813   2.083  0.00  0.00
ATOM  2 CA   CCMT   1  -2.925  -1.739   1.166  0.00  0.00
ATOM  3 CCCMT   1  -1.711  -0.842   0.859  0.00  0.00
ATOM  4 CB   CCMT   1  -4.034  -0.895   1.821  0.00  0.00
ATOM  5 SG   CCMT   1  -4.523   0.408   0.710  0.00  0.00
ATOM  6 SD   CCMT   1  -5.981   1.512   1.567  0.00  0.00
ATOM  7 CE   CCMT   1  -7.394   0.480   1.895  0.00  0.00
ATOM  8 CZ   CCMT   1  -6.988  -0.662   2.846  0.00  0.00
ATOM  9 CH   CCMT   1  -7.604  -2.072   2.895  0.00  0.00
ATOM 10 CH1  CCMT   1  -8.797  -2.090   3.869  0.00  0.00
ATOM 11 CH2  CCMT   1  -8.096  -2.574   1.525  0.00  0.00
ATOM 12 CI   CCMT   1  -5.986  -1.995   4.476  0.00  0.00
ATOM 13 CI1  CCMT   1  -4.582  -2.406   4.958  0.00  0.00
ATOM 14 CI2  CCMT   1  -6.931  -2.001   5.692  0.00  0.00
ATOM 15 CK   CCMT   1  -6.018  -0.615   3.792  0.00  0.00
ATOM 16 NT1  CCMT   1  -6.486  -2.876   3.411  0.00  0.00
ATOM 17 OC1  CCMT   1  -0.511  -1.346   0.867  0.00  0.00
ATOM 18 OC2  CCMT   1  -1.885   0.420   0.592  0.00  0.00
ATOM 19 OT1  CCMT   1  -6.836  -4.122   3.830  0.00  0.00
ATOM 20 HCCMT   1  -1.801  -3.362   1.658  0.00  0.00
ATOM 21 HA   CCMT   1  -3.292  -2.165   0.256  0.00  0.00
ATOM 22 HB1  CCMT   1  -4.878  -1.518   2.033  0.00  0.00
ATOM 23 HB2  CCMT   1  -3.668  -0.468   2.731  0.00  0.00
ATOM 24 HE1  CCMT   1  -7.754   0.067   0.976  0.00  0.00
ATOM 25 HE2  CCMT   1  -8.165   1.065   2.350  0.00  0.00
ATOM 26 HH11 CCMT   1  -9.175  -3.088   3.952  0.00  0.00
ATOM 27 HH21 CCMT   1  -8.875  -1.932   1.170  0.00  0.00
ATOM 28 HH12 CCMT   1  -8.477  -1.749   4.832  0.00  0.00
ATOM 29 HH22 CCMT   1  -7.283  -2.566   0.829  0.00  0.00
ATOM 30 HH13 CCMT   1  -9.567  -1.446   3.500  0.00  0.00
ATOM 31 HH23 CCMT   1  -8.471  -3.571   1.624  0.00  0.00
ATOM 32 HI11 CCMT   1  -4.241  -1.712   5.697  0.00  0.00
ATOM 33 HI21 CCMT   1  -6.956  -2.982   6.119  0.00  0.00
ATOM 34 HI12 CCMT   1  -4.624  -3.387   5.383  0.00  0.00
ATOM 35 HI22 CCMT   1  -6.577  -1.303   6.422  0.00  0.00
ATOM 36 HI13 CCMT   1  -3.906  -2.405   4.128  0.00  0.00
ATOM 37 HI23 CCMT   1  -7.915  -1.722   5.380  0.00  0.00
ATOM 38 HK   CCMT   1  -5.391   0.221   4.019  0.00  0.00
ATOM 39 NNARG   2  -4.657  -5.920   2.257  0.00  0.00
ATOM 40 CA   NARG   2  -3.476  -5.161   2.694  0.00  0.00
ATOM 41 CNARG   2  -3.680  -3.668   2.378  0.00  0.00
ATOM 42 ONARG   2  -4.839  -3.179   2.371  0.00  0.00
ATOM 43 CB   NARG   2  -2.230  -5.679   1.952  0.00  0.00
ATOM 44 CG   NARG   2  -0.992  -4.885   2.410  0.00  0.00
ATOM 45 CZ   NARG   2   2.459  -4.459   1.265  0.00  0.00
ATOM 46 CD   NARG   2   0.254  -5.404   1.668  0.00  0.00
ATOM 47 NE   NARG   2   1.436  -4.648   2.106  0.00  0.00
ATOM 48 NH1  NARG   2   2.406  -4.958   0.025  0.00  0.00
ATOM 49 NH2  NARG   2   3.535  -3.771   1.664  0.00  0.00
ATOM 50 HA   NARG   2  -3.341  -5.287   3.748  0.00  0.00
ATOM 51 HB1  NARG   2  -2.089  -6.716   2.172  0.00  0.00
ATOM 52 HB2  NARG   2  -2.365  -5.552   0.898  0.00  0.00
ATOM 53 HG1  NARG   2  -1.132  -3.847   2.190  0.00  0.00
ATOM 54 HG2  NARG   2  -0.858  -5.011   3.464  0.00  0.00
ATOM 55 HD1  NARG   2   0.393  -6.442   1.888  0.00  0.00
ATOM 56 HD2  NARG   2   0.120  -5.278   0.614  0.00  0.00
ATOM 57 HE   NARG   2   1.475  -4.274   3.033  0.00  0.00
ATOM 58 HH11 NARG   2   1.602  -5.472  -0.274  0.00  0.00
ATOM 59 HH21 NARG   2   3.574  -3.398   2.591  0.00  0.00
ATOM 60 HH12 NARG   2   3.171  -4.817  -0.604  0.00  0.00
ATOM 61 HH22 NARG   2   4.299  -3.631   1.035  0.00  0.00
ATOM 62 H1   NARG   2  -5.466  -5.584   2.740  0.00  0.00
ATOM 63 H2   NARG   2  -4.525  -6.890   2.463  0.00  0.00
ATOM 64 H3   NARG   2  -4.783  -5.802   1.272  0.00  0.00
END



On Wed, Nov 4, 2009 at 7:54 AM, Mark Abraham wrote:

> Chandan Choudhury wrote:
>
>> Hi everyone !!
>>
>> I am having  a problem using pdb2gmx command. Using the command on my
>> input pdb file, it results saying Fatal error: Atom O in residue CCMT 1 not
>> found in rtp entry with 38 atoms while sorting atoms. I do not have only "O"
>> either in input pdb file or in rtp file. and its O and not 0 (zero).
>>
>> My part of input files reads as
>> ATOM  1 NCCMT   1  -2.521  -2.813   2.083  0.00  0.00
>> ATOM  2 CA   CCMT   1  -2.925  -1.739   1.166  0.00  0.00
>> ATOM  3 CCCMT   1  -1.711  -0.842   0.859  0.00  0.00
>> ATOM  4 CB   CCMT   1  -4.034  -0.895   1.821  0.00  0.00
>> ATOM  5 SG

Re: [gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms

2009-11-03 Thread Mark Abraham


Chandan Choudhury wrote:

Hi everyone !!

I am having  a problem using pdb2gmx command. Using the command on my 
input pdb file, it results saying Fatal error: Atom O in residue CCMT 1 
not found in rtp entry with 38 atoms while sorting atoms. I do not have 
only "O" either in input pdb file or in rtp file. and its O and not 0 
(zero).


My part of input files reads as 


ATOM  1 NCCMT   1  -2.521  -2.813   2.083  0.00  0.00
ATOM  2 CA   CCMT   1  -2.925  -1.739   1.166  0.00  0.00
ATOM  3 CCCMT   1  -1.711  -0.842   0.859  0.00  0.00
ATOM  4 CB   CCMT   1  -4.034  -0.895   1.821  0.00  0.00
ATOM  5 SG   CCMT   1  -4.523   0.408   0.710  0.00  0.00
ATOM  6 SD   CCMT   1  -5.981   1.512   1.567  0.00  0.00
ATOM  7 CE   CCMT   1  -7.394   0.480   1.895  0.00  0.00
ATOM  8 CZ   CCMT   1  -6.988  -0.662   2.846  0.00  0.00
ATOM  9 CH   CCMT   1  -7.604  -2.072   2.895  0.00  0.00
ATOM 10 CH1  CCMT   1  -8.797  -2.090   3.869  0.00  0.00
ATOM 11 CH2  CCMT   1  -8.096  -2.574   1.525  0.00  0.00
ATOM 12 CI   CCMT   1  -5.986  -1.995   4.476  0.00  0.00
ATOM 13 CI1  CCMT   1  -4.582  -2.406   4.958  0.00  0.00
ATOM 14 CI2  CCMT   1  -6.931  -2.001   5.692  0.00  0.00
ATOM 15 CK   CCMT   1  -6.018  -0.615   3.792  0.00  0.00
ATOM 16 NT1  CCMT   1  -6.486  -2.876   3.411  0.00  0.00
ATOM 17 OC1  CCMT   1  -0.511  -1.346   0.867  0.00  0.00
ATOM 18 OC2  CCMT   1  -1.885   0.420   0.592  0.00  0.00
ATOM 19 OT1  CCMT   1  -6.836  -4.122   3.830  0.00  0.00
ATOM 20 HCCMT   1  -1.801  -3.362   1.658  0.00  0.00
ATOM 21 HA   CCMT   1  -3.292  -2.165   0.256  0.00  0.00
ATOM 22 HB1  CCMT   1  -4.878  -1.518   2.033  0.00  0.00
ATOM 23 HB2  CCMT   1  -3.668  -0.468   2.731  0.00  0.00
ATOM 24 HE1  CCMT   1  -7.754   0.067   0.976  0.00  0.00
ATOM 25 HE2  CCMT   1  -8.165   1.065   2.350  0.00  0.00
ATOM 26 HH11 CCMT   1  -9.175  -3.088   3.952  0.00  0.00
ATOM 27 HH21 CCMT   1  -8.875  -1.932   1.170  0.00  0.00
ATOM 28 HH12 CCMT   1  -8.477  -1.749   4.832  0.00  0.00
ATOM 29 HH22 CCMT   1  -7.283  -2.566   0.829  0.00  0.00
ATOM 30 HH13 CCMT   1  -9.567  -1.446   3.500  0.00  0.00
ATOM 31 HH23 CCMT   1  -8.471  -3.571   1.624  0.00  0.00
ATOM 32 HI11 CCMT   1  -4.241  -1.712   5.697  0.00  0.00
ATOM 33 HI21 CCMT   1  -6.956  -2.982   6.119  0.00  0.00
ATOM 34 HI12 CCMT   1  -4.624  -3.387   5.383  0.00  0.00
ATOM 35 HI22 CCMT   1  -6.577  -1.303   6.422  0.00  0.00
ATOM 36 HI13 CCMT   1  -3.906  -2.405   4.128  0.00  0.00
ATOM 37 HI23 CCMT   1  -7.915  -1.722   5.380  0.00  0.00
ATOM 38 HK   CCMT   1  -5.391   0.221   4.019  0.00  0.00


What's next in the input PDB file?

Mark


and my part of .rtp file is
[ CCMT ]
 [ atoms ]
 Namber99_34  -0.3961651
 Hamber99_17   0.2951872
CAamber99_11  -0.0735013
HAamber99_19   0.1405104
CBamber99_11  -0.2213715
   HB1amber99_19   0.1465376
   HB2amber99_19   0.1465377
SGamber99_48  -0.2851828
SDamber99_68  -0.089 ;SM
CEamber99_69  -0.10   10
   HE1amber99_70  -0.09   11
   HE2amber99_70  -0.09   12
CZamber99_71  -0.003  13
CHamber99_73   0.334  14
   CH1amber99_74  -0.337  15
  HH11amber99_76   0.090  16
  HH12amber99_76   0.090  17
  HH13amber99_76   0.090  18
   CH2amber99_74  -0.337  19
  HH21amber99_76   0.090  20
  HH22amber99_76   0.090  21
  HH23amber99_76   0.090  22
   NT1amber99_77   0.220  23
   OT1amber99_78  -0.438  24
CIamber99_75   0.329  25
   CI1amber99_74  -0.337  26
  HI11amber99_76   0.090  27
  HI12amber99_76   0.090  28
  HI13amber99_76   0.090  29
   CI2amber99_74  -0.337  30
  HI21amber99_76   0.090  31
  HI22amber99_76   0.090  32
  HI23amber99_76   0.090  33
CKamber99_72  -0.340  34
HKamber99_79   0.162  35
 Camber99_20.643035   36
   OC1amber99_45  -0.7981037
   OC2amber99_45  -0.7981038

Any help is heartly welcomed.
Thanks in advance

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA




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[gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms

2009-11-03 Thread Chandan Choudhury

Hi everyone !!

I am having  a problem using pdb2gmx command. Using the command on my input
pdb file, it results saying Fatal error: Atom O in residue CCMT 1 not found
in rtp entry with 38 atoms while sorting atoms. I do not have only "O"
either in input pdb file or in rtp file. and its O and not 0 (zero).

My part of input files reads as

ATOM  1 NCCMT   1  -2.521  -2.813   2.083  0.00  0.00
ATOM  2 CA   CCMT   1  -2.925  -1.739   1.166  0.00  0.00
ATOM  3 CCCMT   1  -1.711  -0.842   0.859  0.00  0.00
ATOM  4 CB   CCMT   1  -4.034  -0.895   1.821  0.00  0.00
ATOM  5 SG   CCMT   1  -4.523   0.408   0.710  0.00  0.00
ATOM  6 SD   CCMT   1  -5.981   1.512   1.567  0.00  0.00
ATOM  7 CE   CCMT   1  -7.394   0.480   1.895  0.00  0.00
ATOM  8 CZ   CCMT   1  -6.988  -0.662   2.846  0.00  0.00
ATOM  9 CH   CCMT   1  -7.604  -2.072   2.895  0.00  0.00
ATOM 10 CH1  CCMT   1  -8.797  -2.090   3.869  0.00  0.00
ATOM 11 CH2  CCMT   1  -8.096  -2.574   1.525  0.00  0.00
ATOM 12 CI   CCMT   1  -5.986  -1.995   4.476  0.00  0.00
ATOM 13 CI1  CCMT   1  -4.582  -2.406   4.958  0.00  0.00
ATOM 14 CI2  CCMT   1  -6.931  -2.001   5.692  0.00  0.00
ATOM 15 CK   CCMT   1  -6.018  -0.615   3.792  0.00  0.00
ATOM 16 NT1  CCMT   1  -6.486  -2.876   3.411  0.00  0.00
ATOM 17 OC1  CCMT   1  -0.511  -1.346   0.867  0.00  0.00
ATOM 18 OC2  CCMT   1  -1.885   0.420   0.592  0.00  0.00
ATOM 19 OT1  CCMT   1  -6.836  -4.122   3.830  0.00  0.00
ATOM 20 HCCMT   1  -1.801  -3.362   1.658  0.00  0.00
ATOM 21 HA   CCMT   1  -3.292  -2.165   0.256  0.00  0.00
ATOM 22 HB1  CCMT   1  -4.878  -1.518   2.033  0.00  0.00
ATOM 23 HB2  CCMT   1  -3.668  -0.468   2.731  0.00  0.00
ATOM 24 HE1  CCMT   1  -7.754   0.067   0.976  0.00  0.00
ATOM 25 HE2  CCMT   1  -8.165   1.065   2.350  0.00  0.00
ATOM 26 HH11 CCMT   1  -9.175  -3.088   3.952  0.00  0.00
ATOM 27 HH21 CCMT   1  -8.875  -1.932   1.170  0.00  0.00
ATOM 28 HH12 CCMT   1  -8.477  -1.749   4.832  0.00  0.00
ATOM 29 HH22 CCMT   1  -7.283  -2.566   0.829  0.00  0.00
ATOM 30 HH13 CCMT   1  -9.567  -1.446   3.500  0.00  0.00
ATOM 31 HH23 CCMT   1  -8.471  -3.571   1.624  0.00  0.00
ATOM 32 HI11 CCMT   1  -4.241  -1.712   5.697  0.00  0.00
ATOM 33 HI21 CCMT   1  -6.956  -2.982   6.119  0.00  0.00
ATOM 34 HI12 CCMT   1  -4.624  -3.387   5.383  0.00  0.00
ATOM 35 HI22 CCMT   1  -6.577  -1.303   6.422  0.00  0.00
ATOM 36 HI13 CCMT   1  -3.906  -2.405   4.128  0.00  0.00
ATOM 37 HI23 CCMT   1  -7.915  -1.722   5.380  0.00  0.00
ATOM 38 HK   CCMT   1  -5.391   0.221   4.019  0.00  0.00

and my part of .rtp file is
[ CCMT ]
 [ atoms ]
 Namber99_34  -0.3961651
 Hamber99_17   0.2951872
CAamber99_11  -0.0735013
HAamber99_19   0.1405104
CBamber99_11  -0.2213715
   HB1amber99_19   0.1465376
   HB2amber99_19   0.1465377
SGamber99_48  -0.2851828
SDamber99_68  -0.089 ;SM
CEamber99_69  -0.10   10
   HE1amber99_70  -0.09   11
   HE2amber99_70  -0.09   12
CZamber99_71  -0.003  13
CHamber99_73   0.334  14
   CH1amber99_74  -0.337  15
  HH11amber99_76   0.090  16
  HH12amber99_76   0.090  17
  HH13amber99_76   0.090  18
   CH2amber99_74  -0.337  19
  HH21amber99_76   0.090  20
  HH22amber99_76   0.090  21
  HH23amber99_76   0.090  22
   NT1amber99_77   0.220  23
   OT1amber99_78  -0.438  24
CIamber99_75   0.329  25
   CI1amber99_74  -0.337  26
  HI11amber99_76   0.090  27
  HI12amber99_76   0.090  28
  HI13amber99_76   0.090  29
   CI2amber99_74  -0.337  30
  HI21amber99_76   0.090  31
  HI22amber99_76   0.090  32
  HI23amber99_76   0.090  33
CKamber99_72  -0.340  34
HKamber99_79   0.162  35
 Camber99_20.643035   36
   OC1amber99_45  -0.7981037
   OC2amber99_45  -0.7981038

Any help is heartly welcomed.
Thanks in advance

Chandan

-- 
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms

Re: [gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms

Re: [gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms

Re: [gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms

[gmx-users] Fatal error: Atom O in residue CCMT 1 not found in rtp entry with 38 atoms while sorting atoms

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