Your system works for me under Gromacs 4.0.4 - the only issue is that your PDME
residue has a net +0.3 charge. Does your Gromacs installation work properly for
proven systems like proteins?
I would suggest upgrading to version 4.0.4 and trying again. If that does not
work, post to the list a complete description of your hardware and software -
OS, version, compilers used, configuration options, etc, and see if anyone can
spot a problem.
-Justin
Yanmei Song wrote:
Sorry to bother so many times.
I edited the rtp and added the new residue as following, which I think
should be no problem.
[ PDM ]
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
O1 opls_108 -0.300 1
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 O1
O1 +SI1
; Terminal PDMS residue ("beginning" of chain)
[ PDMB ]
[ atoms ]
C1 opls_069 0.000 1
SI1 SI 0.300 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
O1 opls_108 -0.300 1
[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1
; Terminal PDMS residue ("end" of chain)
[ PDME ]
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3
Also my pdb is :
ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00
ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00
ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00
ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00
ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00
ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00
ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00
ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00
ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00
TER
after pdb2gmx, I still got the error:
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
chain #res #atoms
1 ' ' 3 13
All occupancies are one
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
Fatal error:
in .rtp file at line:
-------------------------------------------------------
Anyone knows where I did wrong?
Thank you so much!
On Thu, Apr 30, 2009 at 10:46 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
Yanmei Song wrote:
Hi, Dallas:
I added this to the ffoplsaa.rtp
[ PDM ]
[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1
[ bonds ]
SI O
SI CH3
[ dihedrals ]
CH3 SI O SI dih_PDM_chi1_C_SI_O_SI
SI O SI CH3 dih_PDM_chi1_SI_O_SI_C
O SI O SI dih_PDM_chi1_O_SI_O_SI
The format is the same with other entries. Do you guys think anything
wrong with it?
Also what does it mean by the error message:
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
chain #res #atoms
1 'A' 1 45
All occupancies are one
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
Fatal error:
in .rtp file at line:
-------------------------------------------------------
what is "Source code file: resall.c, line: 289" It seems the problem
comes from here.
That is the line of code that is spotting a problem.
I think the issue is that, in your original .pdb file, you have dozens of
atoms in your polymer chain, all labeled as residue 1. What your .rtp entry
says is that a single PDM should contain only three atoms. Since what you
are trying to do is make a building block, you will need to do several
things:
1. Re-number your .pdb file so that multiple monomers are apparent.
2. Use the + and - characters to indicate connectivity to the next residue
and previous residue, respectively.
3. Create separate .rtp entries for terminal groups, as I suggested
previously, so that termini are handled correctly (since the -n.tdb and
-c.tdb files cannot be used for non-protein).
See the amino acid entries for examples on how to use + and - appropriately,
or the list archive for examples provided by other users for other polymers
(polyethylene is especially common), for example:
http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html
-Justin
Thanks a lot!
On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
<dallas.war...@pharm.monash.edu.au> wrote:
Check consistency with other entries around it, easy way to check to see
that you have the right format.
What did you edit the file with?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file.
[ PDM ]
[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1
[ bonds ]
SI O 0.190 158805.0
SI CH3 0.164 293160.0
[ dihedrals ]
CH3 SI O SI 3.77 3 0
SI O SI CH3 3.77 3 0
O SI O SI 3.77 3 0
On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
<jalem...@vt.edu> wrote:
Yanmei Song wrote:
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
Fatal error:
in .rtp file at line:
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you
created. If you
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Yanmei Song
Department of Chemical Engineering
ASU
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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