Re: vmd-l: Re: VMD-NAMD and PDB element column

From: Francesco Pietra (
Date: Mon Dec 14 2015 - 14:42:21 CST

If relevant, my .gen file with charmm36 of previous post ended with

patch DISU PRA:4 PRA:12
patch DISU PRA:114 PRA:540
patch DISU PRA:298 PRA:332
patch GLUP PRA:235
patch ASPP PRA:516
patch CYSD PRA:503


regenerate angles dihedrals

writepsf ....
writepdb ...


On Mon, Dec 14, 2015 at 4:47 PM, Victor Ovchinnikov <
> wrote:

> Jim et al.,
> From looking at the c40 CHARMM source code, if "PATCH" is supplied then
> dihedrals and/or angles are to be removed and autogenerated after a patch
> is applied. Let me know if you want more details.
> Also, going through the same source code, I did not see CHARMM reading the
> element column from the topology file. Everything past the mass appears to
> be ignored.
> Best,
> Victor
> On 12/14/2015 10:04 AM, Jim Phillips wrote:
>> Also, anybody know what "AUTOGENERATE ANGLES DIHEDRALS PATCH" is supposed
>> to mean in top_all36_na.rtf? (Specifically, what does "PATCH" indicate?)

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