From: Joseph Heil (jpheil_at_ncsu.edu)
Date: Tue Nov 20 2007 - 23:37:32 CST
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
>> !2345678901234567890123456789012345678901234567890123456789012345678901234567890
>>
>> 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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