Re: psfGen error

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Nov 21 2007 - 15:28:22 CST

Psfgen doesn't like atom names that begin with numbers. This is
reserved for patches, where the number in front indicates which
residue each atom comes from.

On Nov 20, 2007, at 11:37 PM, Joseph Heil wrote:

> In case a web browser distorts alignment I've uploaded my files to
> my web page. www4.ncsu.edu/~jpheil
> I suspect the problem is in my topology file but it could easily be
> my pdb file.
>
> thanks,
>
> Joseph
>
> Jeffrey J. Potoff wrote:
>> Hi Joseph,
>> I would check the formating of your PDB file. When I looked at
>> it under another program, the columns were not aligned. The
>> format of the PDB file is very precise, everything must be in the
>> right column and you can't have any <TAB> characters separating
>> entries. Entiries must be separated by <spaces>.
>>
>> Regards,
>> Jeff
>>
>> Joseph Heil wrote:
>>
>>> I am using the psfgen NAMD extension in VMD to try and generate a
>>> psf file for ammonia. I get the error: Warning: failed to set
>>> coordinate for atom 1H MOL:1 U
>>> same problem for the other 2 hyrdogens but not for nitrogen
>>> so I think the error is in my pdb file.
>>> pdb file:
>>> ! 1 2
>>> 3 4 5
>>> 6 7 !
>>> 23456789012345678901234567890123456789012345678901234567890123456789
>>> 01234567890
>>> ATOM 1 N MOL U 1
>>> 0.000 0.000 0.000 1.00
>>> 0.00 N
>>> ATOM 2 1H MOL U 1
>>> -0.000 0.363 1.028 1.00
>>> 0.00 H
>>> ATOM 3 2H MOL U 1
>>> -0.890 0.363 -0.514 1.00
>>> 0.00 H ATOM 4
>>> 3H MOL U 1 0.890
>>> 0.363 -0.514 1.00
>>> 0.00 H
>>> END
>>>
>>> topology file:
>>>
>>> ! 1 2
>>> 3 4
>>> !23456789012345689012345678901234567890
>>> MASS 1 N1 14.01 N
>>> MASS 2 H1 01.008 H
>>> !DEFA FIRS NTER LAST CTER
>>> !AUTO ANGLES DIHE
>>> ! 1 2 3 4
>>> !23456789012345689012345678901234567890
>>> RESI MOL 0.00
>>> GROUP
>>> ATOM N N1 -.600
>>> ATOM 1H H1 +0.200
>>> ATOM 2H H1 +0.200
>>> ATOM 3H H1 +0.200
>>> BOND N 1H N 2H N 3H
>>> DEFA FIRS NTER LAST CTER
>>> AUTO ANGLES DIHE
>>> PATCHING FIRS NONE LAST NONE
>>>
>>> any suggestions on what to change or knowledge on space dependent
>>> formatting of topology files would be greatly appreciated.
>>>
>>> Thank you,
>>>
>>> Joseph Heil
>>> NC State University
>>> College of Textiles
>>> Textile Engineering Chemistry and Science
>>
>>
>>

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