From: TYAGI Abhishek (atyagiaa_at_ust.hk)
Date: Sat Dec 28 2013 - 03:57:56 CST

While performing simulations on NAMD. I am getting following error.

>Main< (2_calibrate) 77 % namd2 eq1.namd > eq1.log
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Structure (psf) file is either in CHARMM format (with
numbers for atoms types, the X-PLOR format using names is required) or the
segment name field is empty.

Charm++ fatal error:
FATAL ERROR: Structure (psf) file is either in CHARMM format (with numbers
for atoms types, the X-PLOR format using names is required) or the segment
name field is empty.

I am not understanding what to do with the error, I tried everything known
to me. If the NAMD uses x-plor files, then why these are not provided with
the tutorial. I tried the DNA and silicon nitride tutorial several times
same error is coming again and again. I had searched this error I observed
that as follows that I don't understand.

"Why does NAMD complain about CHARMM format?

FATAL ERROR: Structure (psf) file is in CHARMM format; XPLOR format required.

CHARMM can create psf files in either CHARMM format (which uses numbers
for atom types) or X-PLOR format (which uses names for atom types). NAMD
uses X-PLOR format both for historical reasons, and because it is more
robust. If NAMD sees a numerical atom type it tries to be helpful with
this message. The solution is to use "write psf card xplor" when creating
the PSF file.

If you did this (or used X-PLOR in the first place) then you probably have
a blank segment name. If you don't specify one, the second column in the
psf file will be blank and NAMD will misread the charge as the atom type.
Fix this by adding name="MAIN" to your segment statement in X-PLOR or
giving the segname as the first argument to GENErate in CHARMM. "

Do anyone have something to tell that will help to resolve this problem. I
am stuck to this point.

Thanks in advance

Abhishek

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