[gmx-users] Error by pdb2gmx
Yanmei Song
ysong30 at asu.edu
Thu Apr 30 00:50:00 CEST 2009
Dear Justin and Dallas:
Thank you for your help earlier.
I made a copy of ffoplsaa.rtp to my working directory and add a new
residue to it. Then perform the following command:
pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/FF.dat
Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43b1 vacuum force field
2: GROMOS96 43a2 force field (improved alkane dihedrals)
3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
7: Encad all-atom force field, using scaled-down vacuum charges
8: Encad all-atom force field, using full solvent charges
6
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:
-------------------------------------------------------
And also my pdb file:
ATOM 1 Si1 PDM A 1 3.796 2.499 -0.834 1.00 0.00
ATOM 2 O2 PDM A 1 4.661 1.181 -0.025 1.00 0.00
ATOM 3 Si4 PDM A 1 4.896 -0.181 1.082 1.00 0.00
ATOM 4 O6 PDM A 1 3.686 -1.442 0.846 1.00 0.00
ATOM 5 Si7 PDM A 1 2.036 -2.061 0.903 1.00 0.00
ATOM 6 O8 PDM A 1 2.038 -3.727 0.331 1.00 0.00
ATOM 7 Si9 PDM A 1 1.180 -5.229 0.010 1.00 0.00
ATOM 8 O10 PDM A 1 2.299 -6.424 -0.637 1.00 0.00
ATOM 9 Si16 PDM A 1 3.364 -7.030 -1.904 1.00 0.00
ATOM 10 O17 PDM A 1 4.537 -5.799 -2.367 1.00 0.00
ATOM 11 Si18 PDM A 1 5.956 -5.364 -3.320 1.00 0.00
ATOM 12 O22 PDM A 1 6.259 -3.637 -3.183 1.00 0.00
ATOM 13 Si24 PDM A 1 5.682 -1.997 -3.451 1.00 0.00
ATOM 14 O26 PDM A 1 6.879 -0.842 -2.885 1.00 0.00
ATOM 15 Si28 PDM A 1 8.515 -0.209 -2.996 1.00 0.00
ATOM 16 O29 PDM A 1 8.808 0.346 -4.640 1.00 0.00
ATOM 17 Si30 PDM A 1 9.879 1.063 -5.838 1.00 0.00
ATOM 18 C34 PDM A 1 9.731 -1.561 -2.566 1.00 0.00
ATOM 19 C36 PDM A 1 8.720 1.221 -1.809 1.00 0.00
ATOM 20 C38 PDM A 1 6.585 -0.914 0.764 1.00 0.00
ATOM 21 C40 PDM A 1 4.835 0.406 2.852 1.00 0.00
ATOM 22 C42 PDM A 1 5.391 -1.730 -5.278 1.00 0.00
ATOM 23 C44 PDM A 1 4.080 -1.754 -2.529 1.00 0.00
ATOM 24 C46 PDM A 1 7.441 -6.315 -2.701 1.00 0.00
ATOM 25 C48 PDM A 1 5.652 -5.789 -5.115 1.00 0.00
ATOM 26 C50 PDM A 1 2.345 -7.495 -3.401 1.00 0.00
ATOM 27 C52 PDM A 1 4.259 -8.545 -1.272 1.00 0.00
ATOM 28 C54 PDM A 1 0.462 -5.872 1.612 1.00 0.00
ATOM 29 C56 PDM A 1 -0.201 -4.930 -1.214 1.00 0.00
ATOM 30 C58 PDM A 1 1.428 -2.016 2.670 1.00 0.00
ATOM 31 C60 PDM A 1 0.900 -1.032 -0.161 1.00 0.00
ATOM 32 O62 PDM A 1 3.063 3.615 0.320 1.00 0.00
ATOM 33 Si63 PDM A 1 1.897 4.001 1.587 1.00 0.00
ATOM 34 O64 PDM A 1 2.116 5.675 2.077 1.00 0.00
ATOM 35 Si68 PDM A 1 3.148 6.934 2.744 1.00 0.00
ATOM 36 C69 PDM A 1 3.682 6.458 4.471 1.00 0.00
ATOM 37 C72 PDM A 1 5.023 3.440 -1.884 1.00 0.00
ATOM 38 C74 PDM A 1 2.464 1.816 -1.948 1.00 0.00
ATOM 39 C76 PDM A 1 0.164 3.775 0.923 1.00 0.00
ATOM 40 C78 PDM A 1 2.137 2.886 3.063 1.00 0.00
ATOM 41 C80 PDM A 1 2.202 8.545 2.805 1.00 0.00
ATOM 42 Si84 PDM A 1 4.922 7.171 1.466 1.00 0.00
ATOM 43 C84 PDM A 1 8.984 1.182 -7.476 1.00 0.00
ATOM 44 C86 PDM A 1 10.387 2.774 -5.280 1.00 0.00
ATOM 45 C88 PDM A 1 11.401 -0.004 -6.037 1.00 0.00
TER
Do you have any idea what I did wrong? It seems the GROMACS doesn't
give the wrong line by
Fatal error:
in .rtp file at line:
-------------------------------------------------------
Thank you so much for your help in advance!
On Tue, Apr 28, 2009 at 4:38 PM, Dallas B. Warren
<Dallas.Warren at pharm.monash.edu.au> wrote:
> That is correct. Fact you can't edit the .rtp file is based on your local computer system permissions. Normally, best idea is to make your own changes to a local copy, and use that.
>
> Catch ya,
>
> Dr. Dallas Warren
> Department of Pharmaceutical Biology and Pharmacology
> Pharmacy and Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at 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-bounces at gromacs.org
>> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
>> Sent: Wednesday, 29 April 2009 9:24 AM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Error by pdb2gmx
>>
>> Dear Dallas:
>>
>> Thanks for your response. It consists of many repeating units. Do you
>> mean I can write the rtp entry for one repeating unit and give it a
>> residue name. After that I need to insert this into the force field
>> rtp file, right? How can I do that? It seems I can not change the rtp
>> file. Thanks.
>>
>> On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren
>> <Dallas.Warren at pharm.monash.edu.au> wrote:
>> > If it is a repeating unit, then you can build a .rtp entry
>> then use it as you would for a protein.
>> >
>> > Catch ya,
>> >
>> > Dr. Dallas Warren
>> > Department of Pharmaceutical Biology and Pharmacology
>> > Pharmacy and Pharmaceutical Sciences, Monash University
>> > 381 Royal Parade, Parkville VIC 3010
>> > dallas.warren at 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-bounces at gromacs.org
>> >> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
>> >> Sent: Wednesday, 29 April 2009 8:59 AM
>> >> To: jalemkul at vt.edu; Discussion list for GROMACS users
>> >> Subject: Re: [gmx-users] Error by pdb2gmx
>> >>
>> >> Dear Justin:
>> >>
>> >> Do you have any suggestions on how I can get the itp and
>> gro file for
>> >> a very long polymer molecules (for example 500 united-atoms), which
>> >> only consists of Si, O and C atom. I can use PRODRG to generate a
>> >> short chain. But PRODRG has limitation of atom numbers in
>> a molecule,
>> >> probably less than 300. So any ideas for building up a long chain
>> >> based on the short chain? By the way, I already have the
>> force field
>> >> parameters.
>> >>
>> >> Thanks a lot!
>> >>
>> >> On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul
>> >> <jalemkul at vt.edu> wrote:
>> >> >
>> >> >
>> >> > Yanmei Song wrote:
>> >> >>
>> >> >> Dear All users:
>> >> >>
>> >> >> I was trying to set up a long chain polymer system. I got the
>> >> >> following PDB file from WebLab. How can I make changes to
>> >> the file in
>> >> >> order to make it as a GROMACS input pdb file. Then I can
>> >> use pdb2gmx
>> >> >> to get the gro, itp and top file.
>> >> >>
>> >> >> When I perform the pdb2gmx command, I got the error message:
>> >> >>
>> >> >> Residue 'MOL' not found in residue topology database
>> >> >>
>> >> >
>> >> > You can't expect pdb2gmx to be magic. A simple search of
>> >> the list archives
>> >> > and wiki will turn up the following:
>> >> >
>> >> >
>> >> http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not
>> > _found_in_residue_topology_database
>> >> >
>> >> > -Justin
>> >> >
>> >> >> Thank you in advance!
>> >> >>
>> >> >> REMARK Created: Tue Apr 28 15:02:20 US Mountain
>> >> Standard Time 2009
>> >> >> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836
>> 1.00 0.00
>> >> >> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027
>> 1.00 0.00
>> >> >> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079
>> 1.00 0.00
>> >> >> ATOM 4 O6 MOL A 1 3.689 -1.438 0.845
>> 1.00 0.00
>> >> >> ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903
>> 1.00 0.00
>> >> >> ATOM 6 O8 MOL A 1 2.039 -3.722 0.332
>> 1.00 0.00
>> >> >> ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014
>> 1.00 0.00
>> >> >> ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633
>> 1.00 0.00
>> >> >> ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900
>> 1.00 0.00
>> >> >> ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365
>> 1.00 0.00
>> >> >> ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320
>> 1.00 0.00
>> >> >> ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185
>> 1.00 0.00
>> >> >> ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453
>> 1.00 0.00
>> >> >> ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890
>> 1.00 0.00
>> >> >> ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003
>> 1.00 0.00
>> >> >> ATOM 16 O29 MOL A 1 8.809 0.341 -4.647
>> 1.00 0.00
>> >> >> ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847
>> 1.00 0.00
>> >> >> ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571
>> 1.00 0.00
>> >> >> ATOM 19 C36 MOL A 1 8.724 1.219 -1.818
>> 1.00 0.00
>> >> >> ATOM 20 C38 MOL A 1 6.589 -0.910 0.760
>> 1.00 0.00
>> >> >> ATOM 21 C40 MOL A 1 4.840 0.411 2.849
>> 1.00 0.00
>> >> >> ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281
>> 1.00 0.00
>> >> >> ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530
>> 1.00 0.00
>> >> >> ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702
>> 1.00 0.00
>> >> >> ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115
>> 1.00 0.00
>> >> >> ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396
>> 1.00 0.00
>> >> >> ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268
>> 1.00 0.00
>> >> >> ATOM 28 C54 MOL A 1 0.463 -5.865 1.617
>> 1.00 0.00
>> >> >> ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209
>> 1.00 0.00
>> >> >> ATOM 30 C58 MOL A 1 1.433 -2.009 2.671
>> 1.00 0.00
>> >> >> ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161
>> 1.00 0.00
>> >> >> ATOM 32 O62 MOL A 1 3.060 3.615 0.318
>> 1.00 0.00
>> >> >> ATOM 33 Si63 MOL A 1 1.891 3.996 1.583
>> 1.00 0.00
>> >> >> ATOM 34 O64 MOL A 1 2.107 5.670 2.078
>> 1.00 0.00
>> >> >> ATOM 35 Si68 MOL A 1 3.135 6.928 2.750
>> 1.00 0.00
>> >> >> ATOM 36 C69 MOL A 1 3.667 6.449 4.477
>> 1.00 0.00
>> >> >> ATOM 37 C72 MOL A 1 5.024 3.447 -1.883
>> 1.00 0.00
>> >> >> ATOM 38 C74 MOL A 1 2.469 1.818 -1.953
>> 1.00 0.00
>> >> >> ATOM 39 C76 MOL A 1 0.160 3.770 0.914
>> 1.00 0.00
>> >> >> ATOM 40 C78 MOL A 1 2.129 2.878 3.056
>> 1.00 0.00
>> >> >> ATOM 41 C80 MOL A 1 2.186 8.538 2.814
>> 1.00 0.00
>> >> >> ATOM 42 Si84 MOL A 1 4.912 7.172 1.476
>> 1.00 0.00
>> >> >> ATOM 43 C84 MOL A 1 8.985 1.172 -7.484
>> 1.00 0.00
>> >> >> ATOM 44 C86 MOL A 1 10.388 2.767 -5.292
>> 1.00 0.00
>> >> >> ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044
>> 1.00 0.00
>> >> >> TER
>> >> >>
>> >> >>
>> >> >
>> >> > --
>> >> > ========================================
>> >> >
>> >> > 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 at gromacs.org
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>> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Yanmei Song
>> >> Department of Chemical Engineering
>> >> ASU
>> >> _______________________________________________
>> >> gmx-users mailing list gmx-users at gromacs.org
>> >> http://www.gromacs.org/mailman/listinfo/gmx-users
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>>
>>
>> --
>> Yanmei Song
>> Department of Chemical Engineering
>> ASU
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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--
Yanmei Song
Department of Chemical Engineering
ASU
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