AMBER Archive (2005)

Subject: AMBER: Re: Problems with ptraj/rdparm

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Fri Jul 15 2005 - 14:22:28 CDT

Lubomir: This didn't seem to make it through to the reflector (probably
due to file size) but I did get it and I will forward my response to the
list (in case others have seen this problem) omitting the attached prmtop
file. What is happening is that the residue names are not being read
correctly in that a residue on the end of the line is adding the first
character of the next line to its name which offsets all of the residue
name reading and leads to junk... The error looks like:

Read in control variables
Read in atom names...
Read in charges...
Read in masses...
Read in IAC (atoms involved in L-J)...
Read in NUMEX (index to excl atom list)...
Read in NNO (index for nonbond of @type)...
Read in residue labels...

Amber8 Module: ptraj

  ILE ARG TRP LYS LEU VAL SER GLU MET LYS
  ALA GLU ASN ILE LYS SER PHE LEU ARG SERP
  HE T HR L YS L EU P RO H ID L EU A LA G LY T HR G
  LU G LN A SN P HE L EU L EU A LA L YS L YS I LEGL
  N TH R GL N TR P LY S LY S PH E GL Y LE U AS P SE
...
  WAT WAT WAT WAT WAT WAT WATW AT W AT W AT W
  AT W AT W AT W AT W AT W AT W AT W AT W AT W AT W
  AT W AT W AT W AT W AT W AT W ATWA T WA T WA T WA
  T WA T WA T WA T WA T WA T WA T WA T WA T WA T WA
  T WA T WA T WA T WA T WA T WA TWAT WAT WAT WAT
   WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
   WRead in the residue to atom pointer list...
Read in bond parameters RK and REQ...

ERROR in scanDouble: ...scanning teq
ERROR in scanDouble: ...scanning teq
ERROR in scanDouble: ...scanning teq

Here is the original message:

> Date: Tue, 12 Jul 2005 17:24:16 +0200
> From: Lubomir Rulisek <lubos_at_uochb.cas.cz>
> To: amber_at_scripps.edu, cheatham_at_chpc.utah.edu
> Subject: Problems with ptraj/rdparm
>
> You may find an attached file - gzipped prmtop - which I am not able
> to read in using ptraj/rdparm module of Amber8. It looks like the
> problem starts with the (mis)interpretation of residue names.
> Not necessary to say that the file was generated by tleap and used
> as topology file in MD simulations.

How exactly did you create this? What is happening is that the final
residue written on each line is written as three characters followed by a
newline rather than 4 characters (the three letters of the name plus a
space) and this is confusing ptraj. It should not confuse FORTRAN
however, but it is not technically the correct format (which is 20A4 or
four characters per residue...)

Are you sure you created this with tleap? If so, I want to know exactly
how so I can try to reproduce. All of my prmtop's seem to have the extra
space and your atom names do have this space so I do not understand why
the residues do not.

I can hack ptraj to overcome this, but before I do I want to understand
whether tleap actually does this or not and on what platform/compiler,
etc.

thanks, tom

p.s. the hack would be in the subroutine NAME_COPY at the top of rdparm.c
to completely change the logic (which as written currently allows newlines
or MS-DOS line terminators in the middle of a name).

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
|
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
|
| tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham

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