Re: Unable to Generate PSF file !

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Jul 04 2005 - 14:01:14 CDT

That's a good question. I don't know for sure.

Please reply to all when responding to messages so that they get posted
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On Jul 4, 2005, at 1:18 PM, Tamal Banerjee wrote:

> hello sir,
>
> I made the psf file !!i think ..it gave me the following result:
> ------------------------
> PSF
>
> 1 !NTITLE
> REMARKS original generated structure x-plor psf file
>
> 20 !NATOM
> 1 A 1 HEX H1A HA -0.030000 1.0080 0
> 2 A 1 HEX H1B HA -0.030000 1.0080 0
> 3 A 1 HEX H1C HA -0.030000 1.0080 0
> 4 A 1 HEX C1 CT3 0.090000 12.0110 0
> 5 A 1 HEX H2A HB -0.030000 1.0080 0
> 6 A 1 HEX H2B HB -0.030000 1.0080 0
> 7 A 1 HEX C2 CT2 0.060000 12.0110 0
> 8 A 1 HEX H3A HB -0.030000 1.0080 0
> 9 A 1 HEX H3B HB -0.030000 1.0080 0
> 10 A 1 HEX C3 CT2 0.060000 12.0110 0
> 11 A 1 HEX H4A HB -0.030000 1.0080 0
> 12 A 1 HEX H4B HB -0.030000 1.0080 0
> 13 A 1 HEX C4 CT2 0.060000 12.0110 0
> 14 A 1 HEX H5A HB -0.030000 1.0080 0
> 15 A 1 HEX H5B HB -0.030000 1.0080 0
> 16 A 1 HEX C5 CT2 0.060000 12.0110 0
> 17 A 1 HEX H6A HA -0.030000 1.0080 0
> 18 A 1 HEX H6B HA -0.030000 1.0080 0
> 19 A 1 HEX H6C HA -0.030000 1.0080 0
> 20 A 1 HEX C6 CT3 0.090000 12.0110 0
>
> 19 !NBOND: bonds
> 1 4 2 4 3 4 5 7
> 6 7 7 4 8 10 9 10
> 10 7 11 13 12 13 13 10
> 14 16 15 16 16 13 17 20
> 18 20 19 20 20 16
>
> 0 !NTHETA: angles
>
>
> 0 !NPHI: dihedrals
>
>
> 6 !NIMPHI: impropers
> 4 1 2 3 7 4 5 6
> 10 7 8 9 13 10 11 12
> 16 13 14 15 20 16 17 18
>
> 0 !NDON: donors
>
>
> 0 !NACC: acceptors
>
>
> 0 !NNB
> -------------------------
> sorry for the missing statements.Please confirm me if this is correct
> form
> of psf for Hexane.It doesnt give any angles or dihedrals.Is this
> because i
> havent mentioned anything in the hexane.inp file?..
> thanks again
> Tamal
>
>> You're missing two key lines before you can write out the psf and pdb.
>>
>> segment A {pdb hexane.pdb}
>> coordpdb hexane.pdb A
>>
>> See the namd tutorial and psfgen manual for more details.
>>
>> -----Original Message-----
>> From: Tamal Banerjee [mailto:tamal_at_iitk.ac.in]
>> Sent: Monday, July 04, 2005 11:35 AM
>> To: JC Gumbart
>> Subject: RE: namd-l: Unable to Generate PSF file !
>>
>> I have opened the tkconsole menu of VMD.
>> and typed the following lines:
>>
>> package require psfgen
>> topology hexane.inp
>> writepdb ubq.pdb
>> writepsf ubq.psf
>>
>> thanks,
>>
>> Tamal
>>
>>
>>> Please list the exact commands you are using to generate the psf.
>>>
>>> -----Original Message-----
>>> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
>>> Behalf
>>> Of Tamal Banerjee
>>> Sent: Monday, July 04, 2005 8:10 AM
>>> To: namd-l_at_ks.uiuc.edu
>>> Subject: namd-l: Unable to Generate PSF file !
>>>
>>> I am a beginner for this NAMD package.
>>> I have sucessfully ran the 1st Tutorial i.e the 1-1 build directory
>>> for
>>> ubliquitin.But when I tried that on a simple molecule like hexane I
>>> was
>>> unable to generate the psf file.The pdb file and the topology file
>>> are
>>> given below.
>>>
>>> pdb file for hexane:
>>>
>>> ATOM 1 C1 HEX 1 -1.374 0.001 -2.632 1.00
>>> ATOM 2 C2 HEX 1 -1.374 0.001 -1.182 1.00
>>> ATOM 3 C3 HEX 1 -0.007 0.001 -0.699 1.00
>>> ATOM 4 C4 HEX 1 -0.007 0.001 0.751 1.00
>>> ATOM 5 C5 HEX 1 1.360 0.001 1.235 1.00
>>> ATOM 6 C6 HEX 1 1.360 0.001 2.685 1.00
>>> ATOM 7 H6A HEX 1 2.387 0.001 3.048 1.00
>>> ATOM 8 H6B HEX 1 0.675 0.001 3.532 1.00
>>> ATOM 9 H6C HEX 1 1.077 1.013 2.395 1.00
>>> ATOM 10 H5A HEX 1 1.873 -0.888 0.872 1.00
>>> ATOM 11 H5B HEX 1 1.485 0.811 0.517 1.00
>>> ATOM 12 H4A HEX 1 -0.241 -0.973 0.324 1.00
>>> ATOM 13 H4B HEX 1 -0.521 0.891 1.114 1.00
>>> ATOM 14 H3A HEX 1 1.019 0.001 -1.062 1.00
>>> ATOM 15 H3B HEX 1 0.233 1.000 -1.062 1.00
>>> ATOM 16 H2A HEX 1 -2.059 0.001 -0.335 1.00
>>> ATOM 17 H2B HEX 1 -1.374 -1.025 -0.819 1.00
>>> ATOM 18 H1A HEX 1 -0.348 0.001 -2.995 1.00
>>> ATOM 19 H1B HEX 1 -2.059 0.001 -3.479 1.00
>>> ATOM 20 H1C HEX 1 -1.888 -0.888 -2.995 1.00
>>>
>>>
>>> Topology file( hexane.inp):
>>>
>>> 27 1
>>> MASS 1 HA 1.008 H !BONDED TO METHYL GROUPS
>>> MASS 2 CT3 12.011 C! METHYL CARBON
>>> MASS 3 HB 1.008 H ! BONDED TO METHYLENE GROUP
>>> MASS 4 CT2 12.011 C ! METHYLENE CARBON
>>>
>>> RESI HEX 0.00 ! HEXANE
>>> GROUP
>>> ATOM H1A HA -0.03
>>> ATOM H1B HA -0.03
>>> ATOM H1C HA -0.03
>>> ATOM C1 CT3 0.09
>>> GROUP
>>> ATOM H2A HB -0.03
>>> ATOM H2B HB -0.03
>>> ATOM C2 CT2 0.06
>>> GROUP
>>> ATOM H3A HB -0.03
>>> ATOM H3B HB -0.03
>>> ATOM C3 CT2 0.06
>>> GROUP
>>> ATOM H4A HB -0.03
>>> ATOM H4B HB -0.03
>>> ATOM C4 CT2 0.06
>>> GROUP
>>> ATOM H5A HB -0.03
>>> ATOM H5B HB -0.03
>>> ATOM C5 CT2 0.06
>>> GROUP
>>> ATOM H6A HA -0.03
>>> ATOM H6B HA -0.03
>>> ATOM H6C HA -0.03
>>> ATOM C6 CT3 0.09
>>> BOND H1A C1 H1B C1 H1C C1 C2 C1
>>> BOND H2A C2 H2B C2 C3 C2
>>> BOND H3A C3 H3B C3 C4 C3
>>> BOND H4A C4 H4B C4 C5 C4
>>> BOND H5A C5 H5B C5 C6 C5
>>> BOND H6A C6 H6B C6 H6C C6
>>> IMPR C1 H1A H1B H1C
>>> IMPR C2 C1 H2A H2B
>>> IMPR C3 C2 H3A H3B
>>> IMPR C4 C3 H4A H4B
>>> IMPR C5 C4 H5A H5B
>>> IMPR C6 C5 H6A H6B
>>> PATCH FIRST NONE LAST NONE
>>>
>>> When we tried to generate the psf file on VMD 1.8.2,it was reading
>>> the
>>> topology file but not generating any data inside the psf file.
>>> Kindly suggest the possible solution.
>>>
>>> thanks
>>>
>>> Tamal
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>

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