From: Evandro Semighini (epsemighini_at_gmail.com)
Date: Thu Apr 16 2015 - 15:28:23 CDT
Hello,
I'm using NAMD 2.10.
I searched and found this threads:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/20015.html
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/2881.htm=
l
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/20301.html
I changed the first line of the psf file to put the NAMD CMAP terms but
things goes the same way as before.
I tried with 4 diferent molecules and all of them get some bond or vdW
error.
I tried to generate the prm and rtf files with MATCH, I was able to run
psfgen with it, but I got vdW errors.
As far as I saw with the ParamChem and VegaZZ, the softwares are not
recognizing the "UNK" residue.
I'm guessing I'll have to follow the "how to parametrize new ligands"
tutorial and split my molecules into "residues", draw them, put the data
from ParamChem and see if it works. Do you think it can work, without the
need of Spartan ?
FFtk asks me to use Gaussian, which I also don't have.
I'm sorry if I look lame, but I'm completely lost.
Thank you for the help.
Evandro
---- here some part of the psf file I used
PSF NAMD CMAP
3 !NTITLE
* GENERATED BY CHARMM-GUI (http://WWW.CHARMM-GUI.ORG) VERSION ON APR, 15.
2015.
* READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY
FILE
* DATE: 4/15/15 14:23:46 CREATED BY USER:
charmm-gui
64 !NATOM
1 Z1 1 UNK C14 CG311 -0.102000
12.0110 0 0.00000 -0.301140E-02
2 Z1 1 UNK N1 NG311 -0.446000
14.0070 0 0.00000 -0.301140E-02
3 Z1 1 UNK H1 HGA1 0.900000E-01
1.00800 0 0.00000 -0.301140E-02
4 Z1 1 UNK H22 HGPAM1 0.338000
1.00800 0 0.00000 -0.301140E-02
5 Z1 1 UNK C25 CG2R61 0.108000
12.0110 0 0.00000 -0.301140E-02
6 Z1 1 UNK C20 CG2R61 -0.300000E-02
12.0110
69 !NBOND: bonds
41 43 41 42 43 45 1 3
1 2 1 16 16 17
16 7
2015-04-16 16:53 GMT-03:00 Evandro Semighini <epsemighini_at_gmail.com>:
> Hello,
>
> I'm using NAMD 2.10.
> I searched and found this threads:
>
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/20015.html
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/2881.html
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/20301.html
>
> I changed the first line of the psf file to put the NAMD CMAP terms but
> things goes the same way as before.
> I tried with 4 diferent molecules and all of them get some bond or vdW
> error.
>
> I tried to generate the prm and rtf files with MATCH, I was able to run
> psfgen with it, but I got vdW errors.
>
> As far as I saw with the ParamChem and VegaZZ, the softwares are not
> recognizing the "UNK" residue.
>
> I'm guessing I'll have to follow the "how to parametrize new ligands"
> tutorial and split my molecules into "residues", draw them, put the data
> from ParamChem and see if it works. Do you think it can work, without the
> need of Spartan ?
>
> FFtk asks me to use Gaussian, which I also don't have.
>
> I'm sorry if I look lame, but I'm completely lost.
>
> Thank you for the help.
>
> Evandro
>
>
>
>
> 2015-04-15 17:44 GMT-03:00 Bennion, Brian <bennion1_at_llnl.gov>:
>
> Hello,
>>
>> which version namd are you using. searching the vmd-l list or namd-l
>> should show that you need to put the key word, NAMD, in the psf file so
>> that namd can accept the large atom types.
>>
>> If you get large errors from the paramchem.org website for your
>> molecule, then FFTK in VMD is the only real way to get viable parameters--001a11c383ce2b7d6f0513dd4e9e--
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