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#12211 - 10/31/06 08:22 AM "fmt: read unexpected character" error with PHENYLGLYCINE MolDyn
tarajano Offline
Forum Member

Registered: 12/29/05
Posts: 33
Loc: Spain
hello all :

im working with peptides having the "rare" aminoacid phenylglycine . I have been googling for a while and have found a helpfull file (http://www.cs.washington.edu/homes/tapan/projects/GBP/figures/AMINOH.RTF)
containing an old topology for this residue.

well i have modified some atom-type definitions at tis file to make it compatible with my charmm 30b1 and when i start the MD run i receive the following error :
##########################
1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 30b1 August 15, 2003
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: Linux-2.6.15-23-686(i686)@localhost.localdom
Created on 10/30/ 6 at 13:27:24 by user: tarajano

Maximum number of ATOMS: 25140, and RESidues: 14000
Current HEAP size: 2048000, and STACK size: 500000

RDTITL> * DYNAMIC FOR THE PGY AT 300K
RDTITL> *

CHARMM>

CHARMM> !Este es el input de la dinamica molecular para pgy
CHARMM>

CHARMM> open unit 1 card read name topol_amino_rtf.inp
VOPEN> Attempting to open::topol_amino_rtf.inp::
OPNLGU> Unit 1 opened for READONLY access to topol_amino_rtf.inp

CHARMM> read RTF card unit 1
MAINIO> Residue topology file being read from unit 1.
TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
TITLE> * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED
TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN
TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL
TITLE> *

CHARMM> close unit 1
VCLOSE: Closing unit 1 with status "KEEP"

CHARMM>

CHARMM> open unit 1 card read name param19_eef1.inp
VOPEN> Attempting to open::param19_eef1.inp::
OPNLGU> Unit 1 opened for READONLY access to param19_eef1.inp

CHARMM> read PARA card unit 1

PARAMETER FILE BEING READ FROM UNIT 1
TITLE> * - PARAMETER FILE PARAM19 * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
TITLE> *
PARRDR> NOTE: atom type "CR " is removed from previous group
PARRDR> NOTE: atom type "OC " is removed from previous group
PARRDR> NOTE: atom type "OT " is removed from previous group
PARRDR> NOTE: atom type "OH2 " is removed from previous group
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

CHARMM> close unit 1
VCLOSE: Closing unit 1 with status "KEEP"

CHARMM>

CHARMM> open unit 1 card read name "pgy.ent"
VOPEN> Attempting to open::pgy.ent::
OPNLGU> Unit 1 opened for READONLY access to pgy.ent

CHARMM> read sequ pdb unit 1
MAINIO> Sequence information being read from unit 1.
TITLE> *
fmt: read unexpected character
apparent state: internal I/O
last format: (6X,I5,1X,A4,1X,A4,2X,A4,3X,3F8.3,6X,F6.2,6X,A4)
lately reading sequential formatted internal IO
Aborted
##########################

the topology file im using is:
@@@@@@@@@@@@@@@@@@@@@@@
* TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
* T. Lazaridis: here the ionic sidechains and termini are neutralized
* Also, a new atom type has been added, CR, for 4-bonded carbon in
* aromatics and Arginine. Modifications are marked by TL
*
20 1 ! Version number
MASS 1 H 1.00800 ! hydrogen which can h-bond to neutral atom
MASS 2 HC 1.00800 ! - " - charged atom
MASS 3 HA 1.00800 ! aliphatic hydrogen
MASS 4 HT 1.00800 ! TIPS3P WATER HYDROGEN
MASS 5 LP 0.0 ! ST2 LONE PAIR
MASS 10 CT 12.01100 ! aliphatic carbon
MASS 11 C 12.01100 ! carbonyl carbon
MASS 12 CH1E 13.01900 ! extended atom carbon w/ one hydrogen
MASS 13 CH2E 14.02700 ! - " - two
MASS 14 CH3E 15.03500 ! - " - three
MASS 15 CR1E 13.01900 ! - " - in aromatic ring w/ one H
MASS 16 CM 12.01100 ! carbon in carbonmonoxide
MASS 31 N 14.00670 ! peptide nitrogen with no hydrogens attached
MASS 32 NR 14.00670 ! nitrogen in aromatic ring with no hydrogens
MASS 33 NP 14.00670 ! pyrole nitrogen
!MASS 34 NH1E 15.01470 ! extended atom peptide nitrogen with one hydrogen
!MASS 35 NH2E 16.02270 ! - " - two -"-
!MASS 36 NH3E 17.03070 ! - " - three -"-
!MASS 37 NC2E 16.02270 ! extended atom charged guanidinium nitrogen w/ 2 H
MASS 38 NH1 14.00670 ! peptide nitrogen bound to one hydrogen
MASS 39 NH2 14.00670 ! - " - two -"-
MASS 40 NH3 14.00670 ! nitrogen bound to three hydrogens
MASS 41 NC2 14.00670 ! charged guanidinuim nitrogen bound to two hydrogens
MASS 51 O 15.99940 ! carbonyl oxygen
MASS 52 OC 15.99940 ! carboxy oxygen
!MASS 53 OH1E 17.00740 ! extended atom hydroxy oxygen
!MASS 54 OH2E 18.01540 ! extended atom water
MASS 55 OH1 15.99940 ! hydroxy oxygen
MASS 56 OH2 15.99940 ! ST2 water oxygen
MASS 57 OM 15.99940 ! oxygen in carbonmonoxide
MASS 58 OT 15.99940 ! TIPS3P WATER OXYGEN
MASS 59 OS 15.99940 ! ester oxygen
MASS 81 S 32.06000 ! sulphur
MASS 82 SH1E 33.06800 ! extended atom sulphur with one hydrogen
MASS 91 FE 55.84700 ! iron
MASS 92 CR 12.01100 ! 4-bonded carbon in aromatics and Arginine

DECL -C
DECL -O
DECL +N
DECL +H
DECL +CA

AUTOGENERATE ANGLES
DEFA FIRS NTER LAST CTER

!PGY

RESI PGY 0.00 ! Phenylglycine
GROUP
ATOM N NP -0.40
ATOM HN H 0.25
ATOM CA CT 0.05
ATOM HA HA 0.05
GROUP
ATOM CB CR 0.00
ATOM CG1 CR1E -0.13
ATOM HG1 HA 0.13
ATOM CG2 CR1E -0.13
ATOM HG2 HA 0.13
GROUP
ATOM CD1 CR1E -0.13
ATOM HD1 HA 0.13
ATOM CD2 CR1E -0.13
ATOM HD2 HA 0.13
ATOM CE CR1E -0.13
ATOM HE HA 0.13
GROUP
ATOM C C 0.60
ATOM O O -0.55
BOND CB CA CG1 CB CG2 CB CD1 CG1
BOND CD2 CG2 CE CD1 CE CD2 N HN
BOND N CA O C C CA C +N CA HA
BOND CG1 HG1 CG2 HG2 CD1 HD1
BOND CD2 HD2 CE HE
!DIHE -C N CA C N CA C +N CA C +N +CA
!DIHE CG1 CB CA N
IMPH CD1 CG1 CB CG2 CD2 CG2 CB CG1 CE CD1 CG1 CB
IMPH CE CD2 CG2 CB CD2 CE CD1 CG1 N -C CA HN
IMPH CB CG1 CG2 CA CG1 CB CD1 HG1 CG2 CB CD2 HG2
IMPH CD1 CE CD2 CG2 CD1 CG1 CE HD1 CD2 CG2 CE HD2
IMPH CE CD1 CD2 HE C CA +N O
DONO HN N
ACCE O C
IC -C CA *N HN 0.0000 0.00 180.00 0.00 0.0000
IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000
IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000
IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000
IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000
IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000
IC N C *CA HA 0.0000 0.00 240.00 0.00 0.0000
IC N CA CB CG1 0.0000 0.00 240.00 0.00 0.0000 ! 90.0?
IC CG1 CA *CB CG2 0.0000 0.00 180.00 0.00 0.0000
IC CA CB CG1 CD1 0.0000 0.00 180.00 0.00 0.0000
IC CD1 CB *CG1 HG1 0.0000 0.00 180.00 0.00 0.0000
IC CA CB CG2 CD2 0.0000 0.00 180.00 0.00 0.0000
IC CD2 CB *CG2 HG2 0.0000 0.00 180.00 0.00 0.0000
IC CB CG1 CD1 CE 0.0000 0.00 0.00 0.00 0.0000
IC CE CG1 *CD1 HD1 0.0000 0.00 180.00 0.00 0.0000
IC CE CG2 *CD2 HD2 0.0000 0.00 180.00 0.00 0.0000
IC CD1 CD2 *CE HE 0.0000 0.00 180.00 0.00 0.0000
@@@@@@@@@@@@@@@@@@@@@@@

my pdb is:

!!!!!!!!!!!!!!!!!!!!
ATOM 1 N PGY 1 -1.946 -0.036 2.494

ATOM 2 CA PGY 1 -1.744 1.381 2.290

ATOM 3 C PGY 1 -2.513 1.807 1.050

ATOM 4 O PGY 1 -3.246 2.801 1.052

ATOM 5 CB PGY 1 -0.327 1.792 2.259

ATOM 6 C PGY 1 0.771 0.892 2.206

ATOM 7 C PGY 1 2.090 1.360 2.252

ATOM 8 C PGY 1 2.347 2.730 2.343

ATOM 9 C PGY 1 1.284 3.637 2.389

ATOM 10 C PGY 1 -0.035 3.172 2.350

END
!!!!!!!!!!!!!!!!!!!!

does anybody has an idea of what could be going wrong here?
if i have not been clear enough please let me know

best regards 2 all

tarajano

PS: Im not quite sure about how will i receive ur anserws
so u can reply to tarajano@bioinfo.cu

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#12212 - 10/31/06 08:39 AM Re: "fmt: read unexpected character" error with PHENYLGLYCINE MolDyn [Re: tarajano]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
There is a problem with your pdb-file, which contains an unexpected character. Is it in the correct format according to the PDB specifications, and does if follow unix "standards" for text files (ie, if you worked on it with Windows/DOS editor it may contain unexpected characters)? If you give the CHARMM command WRITE COOR PDB NAME TEST.PDB after the PSF is generated you can see what CHARMM expects the file to look like.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#12213 - 11/01/06 08:54 AM Re: "fmt: read unexpected character" error with PHENYLGLYCINE MolDyn [Re: lennart]
tarajano Offline
Forum Member

Registered: 12/29/05
Posts: 33
Loc: Spain
hi again lennart:

your right about the windows editor, i have generated my pdb file in Windows and i have also read and modified the the pdb file in windows, but it seems strange to me that vim does not "see" those posible "rare" characters that charmm is complaining about.

i have followed ur instructions about the command
_write coor pdb name test.pdb_ after generating the PSF file
but unfortunately my script dies while its still reading the
seq from pdb file

e.g:
********************************************************
CHARMM> read sequ pdb unit 1
MAINIO> Sequence information being read from unit 1.
TITLE> *
fmt: read unexpected character
apparent state: internal I/O
last format: (6X,I5,1X,A4,1X,A4,2X,A4,3X,3F8.3,6X,F6.2,6X,A4)
lately reading sequential formatted internal IO
Aborted
********************************************************

i send u again part of my charmm script:

####################
open unit 1 card read name pgy_toph19_eef1.inp
read RTF card unit 1
close unit 1

open unit 1 card read name param19_eef1.inp
read PARA card unit 1
close unit 1

open unit 1 card read name "pgy.pdb"
read sequ pdb unit 1
generate prot setu

! pdb
open unit 1 card read name "pgy.pdb"
read coor pdb unit 1
close unit 1

open write formatted unit 27 name pgykpmd.psf
write psf card unit 27
write coor pdb name test.pdb ! line suggested by LennartNilson
open unit 1 card write name "pgykmd.pdb"
write coor pdb unit 1
close unit 1
####################

i really dont know if the commands are in a wrong order at the script , but i think this is not the case 'cos i have used it many times before to simulate other peptides

perhaps could be a problem related to the topology file which i have had to build it by myself cos im dealing with a "rare" aminoacid, but as far as charmm doesnot complains about topology im not sure that the error could be there.

The other thing i am suspecting of is my initial pdb file.
I have noted that programs such as SwissPDBViewer and Rasmol do not represent double bonds at the aromatic ring of phenylglycine. (i have previusly sent my pdb file if you want u can take a look)

well after all this .. im still trying to look for the solution .. if u or anyone have any other advice to me i will really preciate it


thatnks in advence

manuel





i preciate ur help to me .

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#12214 - 11/01/06 09:24 AM Re: "fmt: read unexpected character" error with PHENYLGLYCINE MolDyn [Re: tarajano]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
It is not CHARMM, but the fortran compiler that complains.
Did you fix the file problem? If not it is not surprising that the error remains.
You can either write the file again in a unix editor, or use a command like dos2unix that is often found on unix systems.
You do not have to read the sequence from the PDB file, you can also specify it in the input file to the CHARMM job (see examples in the Script Archive).
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#12215 - 11/01/06 11:32 AM Re: "fmt: read unexpected character" error with PHENYLGLYCINE MolDyn [Re: tarajano]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
Also, 'vim' is a fairly intelligent editor, and may handle the DOS/Unix differences gracefully, while that's not the case for formatted Fortran I/O such as CHARMM reading a file.
_________________________
Rick Venable
computational chemist


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#12216 - 11/06/06 12:10 PM Re: "fmt: read unexpected character" error with PHENYLGLYCINE MolDyn [Re: rmv]
tarajano Offline
Forum Member

Registered: 12/29/05
Posts: 33
Loc: Spain
hi again ... my "fmt: read unexpected character" error was generated by format errors in the pdb input file..
the problem is that the program i used to build the phenylglycine residue wasnt capable to generate a "good" pdb file. so charmm complains...
here im standing at the initial place of my problem :

!__obtain a good phenylglycine model___!

ive tried to build an alpha helix using gen-alpha-helix.inp" (from our friend Lennart) and using a topology file that i made from an old topology file for PGY ...
the result was a total failure at the PGY coordenades.. and evidently this is cos my topology is not good at all..
had somebady previously worked with phenylglycine ?
i really need help to obtain the topology for this residue .
i succed building a topol for norleucine .. but my aromatic friend PGY tends to be quite harder

hi 2 all

tarajano

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#12217 - 11/06/06 12:30 PM Re: "fmt: read unexpected character" error with PHENYLGLYCINE MolDyn [Re: tarajano]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
The atom names for PGY in your PDB file do not appear to conform exactly to those in the RESIdue description; the PDB file seems to contain many atoms identified as simply 'C', which won't work; that name is reserved for the amide linkage carbonyl C atom only.
_________________________
Rick Venable
computational chemist


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#12218 - 11/06/06 02:11 PM Re: "fmt: read unexpected character" error with PHENYLGLYCINE MolDyn [Re: rmv]
tarajano Offline
Forum Member

Registered: 12/29/05
Posts: 33
Loc: Spain
that's right .. thats the very problem.
but the fact is that the prog i used to build my PGY pdb did not built a "good" pdb file...

(offtopic..do u know any linux/free software that could help me to contruct 3D models for proteins?)

Ive tried to use "gen-alpha-helix.inp" but ive noticed that the topology file I built for PGY doesnt work ... the output
for "gen-alpha-helix.inp" at PGY atoms is a mess.

################
11 ATOM 9 N PGY 2 3.333 1.550 0.000 1.00 0.00 HLX
12 ATOM 10 H PGY 2 3.907 0.756 0.000 1.00 0.00 HLX
13 ATOM 11 CA PGY 2 3.925 2.874 0.000 1.00 0.00 HLX
14 ATOM 12 CB PGY 2 9999.0009999.0009999.000 1.00 0.00 HLX
15 ATOM 13 CG1 PGY 2 9999.0009999.0009999.000 1.00 0.00 HLX
16 ATOM 14 CG2 PGY 2 9999.0009999.0009999.000 1.00 0.00 HLX
17 ATOM 15 CD1 PGY 2 9999.0009999.0009999.000 1.00 0.00 HLX
18 ATOM 16 CD2 PGY 2 9999.0009999.0009999.000 1.00 0.00 HLX
19 ATOM 17 CE PGY 2 9999.0009999.0009999.000 1.00 0.00 HLX
20 ATOM 18 C PGY 2 3.450 3.699 -1.185 1.00 0.00 HLX
21 ATOM 19 O PGY 2 3.065 4.859 -1.048 1.00 0.00 HLX
22 ATOM 20 N ALA 3 3.467 3.120 -2.382 1.00 0.00 HLX
23 ATOM 21 H ALA 3 3.777 2.194 -2.475 1.00 0.00 HLX
24 ATOM 22 CA ALA 3 3.026 3.857 -3.551 1.00 0.00 HLX
################

do u have ever worked with this residue or do u know where to find a suitable topology for it?

otherwise i will continue hitting my head trying to write
such a funny thing as a topology file is

thnks in advvance
tarajano

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#12219 - 11/06/06 02:39 PM Re: "fmt: read unexpected character" error with PHENYLGLYCINE MolDyn [Re: tarajano]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
It would appear you may be trying to use IC BUILD without properly cleaning up the IC table entries in the PGY RESIdue description. As an alternative, you could probably also fix the atom name labels in your PDB file. Work with a simple system like ALA-PGY-ALA until you get this correct before proceeding with a protein.
_________________________
Rick Venable
computational chemist


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