AMBER Archive (2004)

Subject: AMBER: NMODE for protein via MM-PBSA-cntd

From: ML (
Date: Wed Feb 04 2004 - 10:09:57 CST

Dear Holger and MM-PBSA/nmode team,
I am trying to calculate normal modes using nmode via mm-pbsa for a
3200-atom protein. With the help from the AMBER e-mail archive, I was
able to compile AMBER7 on 64-bit AMD Opterons for this system.

To hold down the memory needed for nonbond pairlist, I adjusted script to read in cutoff for nonbonded interactions. Sander
minimization goes fine until gradient of 10E-4 (or even 10E-5) but nmode
starts with a 10* or so worse gradient and fails! (How do sander and
nmode calculate rms gradients? Do they differ in that? Why?)

I went into modyfying again to allow for Newton-Raphson
minimizations in nmode. Now it works, I just wonder how long it

Is there any other way around to avoid Newton-Raphson? An idea is to
minimize by sander until 10E-6 or -7 but I am not sure if it'd help.

Best regards,

   Martin Lepsik

Holger Gohlke wrote:

>ML schrieb:
>>Hello AMBER team!!!
>>Is there any way to do nmode calculations via mm-pbsa stepwise? I mean
>>steep desc+conj.grad. mini in sander, then Newt-Raph mini in nmode, then
>>normal modes in nmode. What it does now is passing minimization commands
>>to sander and urging nmode to do normal mode analysis, not Newt-Rap.
>Not without changing the code. Starting points would be the
>"create_nmode_input" subroutine, where you would have to add another
>input file for nmode to do NR-minimization. Then, another system call to
>nmode has to be added to the subroutine "calc_NM" (plus adaptation of
>the used filenames). But before you start, please consider that
>NR-minimization can be computationally demanding for larger systems (in
>fact, this is the reason why your suggested route hasn't been put into
>Best regards
>>I'd very much appreciate your help.
>>Martin Lepsik
>>Martin Lepsik
>>Dept. of Molecular Modeling
>>Institute of Organic Chemistry & Biochemistry
>>Czech Academy of Sciences
>>phone: +420-220 183 540
>>fax:+420-220 183 292
>>The AMBER Mail Reflector
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