[gmx-users] Error while running grompp for em (MD) in Urea
Anil Kumar
anil at chem.iitb.ac.in
Sat May 12 13:29:40 CEST 2007
Dear All,
Can anyone help me in running simulation in explicit urea.
When i was using urea+h2o.gro and urea.itp and tried to do simulation in
explicit urea.
After doing genbox, i am not able to do the grompp for energy minimization
and getting the error which is given below.
I have added masses of all the atoms of urea in atommass.dat file, but
still getting the same error.
Please help me, where does am i making the mistakes.
processing coordinates...
Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2)
Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3)
Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2)
Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3)
Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2)
Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3)
Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2)
Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3)
Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2)
Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3)
Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2)
Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3)
Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2)
(more than 20 non-matching atom names)
WARNING 3 [file "base.top", line 808]:
6150 non-matching atom names
atom names from base.top will be used
atom names from after_sol.gro will be ignored
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
# BONDS: 945
# G96BONDS: 128
# ANGLES: 1215
# G96ANGLES: 190
# PDIHS: 1134
# IDIHS: 485
# LJ14: 1242
# SETTLE: 2050
ERROR 4 [file "base.top", line 808]:
atom C1 (Res UREA-11) has mass 0
ERROR 5 [file "base.top", line 808]:
atom O2 (Res UREA-11) has mass 0
ERROR 6 [file "base.top", line 808]:
atom N3 (Res UREA-11) has mass 0
ERROR 7 [file "base.top", line 808]:
atom H4 (Res UREA-11) has mass 0
ERROR 8 [file "base.top", line 808]:
atom H5 (Res UREA-11) has mass 0
ERROR 9 [file "base.top", line 808]:
atom N6 (Res UREA-11) has mass 0
ERROR 10 [file "base.top", line 808]:
atom H7 (Res UREA-11) has mass 0
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: fatal.c, line: 416
Fatal error:
Too many warnings, grompp terminated
-------------------------------------------------------
"I'm An Oakman" (Pulp Fiction)
Thanks in advance.
With Warm Regards
anil
--
(¨`•.•´¨) Always
`•.¸(¨`•.•´¨) Keep
(¨`•.•´¨)¸.•´ Smiling!
`•.¸.•´
«•´`•.(*•.¸(`•.¸ ¸.•´)¸.•*).•´`•»
«•´¨*•.¸¸. * ANIL *.¸¸.•*¨`•»
«•´`•.(¸.•´(¸.•* *•.¸)`•.¸).•´`•»
ANIL KUMAR(Research Scholar),
Bio-Organic Lab No-336(2nd Floor),
Dept. of Chemistry,I.I.T.Bombay,Powai,
Mumbai-400076,
Ph. No.-022-25764780(Lab)
-----------------------------------------
Residence:-
Hostel#1,Room#297,IIT Bombay,Powai,
Mumbai-400076,Ph.No.:-022-25721017(Hostel)
-------------------------------------------------
Web:http://chemanil.googlepages.com/
--------------------------
"Education is a progressive discovery of our ignorance"
- Will Durant
----------------------------
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> Today's Topics:
>
> 1. Re: CNT Potassium doping with GROMACS (George Abadir)
> 2. Re: Cannot find fftw3f (Mark Abraham)
> 3. Re: suggest small revision to genbox (bharat v. adkar)
> 4. Re: suggest small revision to genbox (David van der Spoel)
> 5. Error while running MD in DMSO! (Anil Kumar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 11 May 2007 18:52:43 -0700
> From: George Abadir <georgea at ece.ubc.ca>
> Subject: Re: [gmx-users] CNT Potassium doping with GROMACS
> To: georgea at ece.ubc.ca, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <46451DEB.3090800 at ece.ubc.ca>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Another point: is it possible to use pdb2gmx to do the job instead of
> x2top? I tried and used the GROMOS96 43b1 vacuum force field (since the
> doping by potassium is in vacuum), but i got the error"Residue 'CNT' not
> found in residue topolgy database'. I went to the 'ffg43b1.rtp' file in
> the /share/top folder and defined it as '[CNT]
>
>
> [atoms]
>
>
> C C 0 0'
> but still get the same error.
> Your help is much appreciated,
> Thank you in advance,
> George
>
> George Abadir wrote:
>
>> Hi,
>> I want to make a simulation of CNT in an environment of potassium
>> atoms to see how they will be adsorbed on the CNT surface (this is a
>> way of doping carbon nanotubes). I built a .pdb file with a CNT and
>> some potassium atoms with random coordinates around the nanotube. When
>> I run x2top to have my topology file, I get the error:"No forcefield
>> type for atom K with 0 bond". The problem is that the atoms of
>> potassium should indeed be not bonded to anything at the beginning of
>> the simulation. Does anybody have a way to describe such a system and
>> avoid this error?
>> Thank you very much in advance,
>> Regards,
>> George
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>>
>>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 12 May 2007 12:22:41 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Cannot find fftw3f
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <464524F1.8000503 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Omovie, Sheyore John wrote:
>> Hi,
>> Even after following the instructions in the HowTo Cygwin and gromacs, I
>> still come up
>> with the configure error:Cannot find fftw3f.
>
> The most likely thing is that you haven't actually followed the
> instructions precisely...
> http://www.gromacs.org/pipermail/gmx-users/2006-April/021147.html In
> particular you need "--enable-float" with configure for fftw.
>
>> I ahve also tried specifying the header file directory, it still doesn't
>> work.
>
> No, that wouldn't help.
>
>> I would appreciate any advice on overcoming this problem.
>
> In the absence of more information from you, all I can suggest is trying
> again :-) In extremis, re-installing cygwin has helped another user.
>
> Mark
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 12 May 2007 12:05:44 +0530 (IST)
> From: "bharat v. adkar" <bharat at sscu.iisc.ernet.in>
> Subject: Re: [gmx-users] suggest small revision to genbox
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <Pine.LNX.4.64.0705121155010.19935 at sscu.iisc.ernet.in>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
>
> genbox works fine for me. i use 3.3.1 version. it works fine with and
> without script.
>
> but i don't understand how will u get rid of backup files in the permanent
> directory from whatever u have mentioned, because gromacs creates the
> output topology in the same location where it reads the input topology
> from. so temperory directory thing will work only if u make an link of top
> file from permanent directory and use this linked version as input, then
> move the new top from temp to permanent directory.
>
> bharat
>
>
>
>
>
> On Fri, 11 May 2007, David Mobley wrote:
>
>> All,
>>
>> I'm trying to write some wrappers to set up a project using standard
>> gromacs tools. Anyway, it looks to me like genbox is not handling its
>> path names correctly. In particular, here's what I did:
>>
>> - Make temporary directory in which to run genbox
>> - Move to temporary directory, run genbox (reading input files from
>> permanent directory; writing input files to permanent directory)
>> - Change back to starting directory; delete temporary directory
>>
>> When I do this, I get a blank output topology file in my permanent
>> directory.
>>
>> It appears what's going on is that the file temp.top is written into
>> my temporary directory, but never moved into the permanent directory;
>> I suspect genbox is not handling the absolute/relative path issue
>> correctly here?
>>
>> I can work around, but this is just a bit annoying -- when I script
>> it, I end up with a bunch of "#temp.top.1#" etc files in my working
>> directory if I use editconf in the normal way, which is why I was
>> using the temporary directory thing to begin with.
>>
>> Thanks,
>> David
>> _______________________________________________
>> gmx-users mailing list gmx-users at 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 12 May 2007 11:13:00 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] suggest small revision to genbox
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4645851C.2020301 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> David Mobley wrote:
>> All,
>>
>> I'm trying to write some wrappers to set up a project using standard
>> gromacs tools. Anyway, it looks to me like genbox is not handling its
>> path names correctly. In particular, here's what I did:
>>
>> - Make temporary directory in which to run genbox
>> - Move to temporary directory, run genbox (reading input files from
>> permanent directory; writing input files to permanent directory)
>> - Change back to starting directory; delete temporary directory
>>
>> When I do this, I get a blank output topology file in my permanent
>> directory.
>>
>> It appears what's going on is that the file temp.top is written into
>> my temporary directory, but never moved into the permanent directory;
>> I suspect genbox is not handling the absolute/relative path issue
>> correctly here?
>>
>> I can work around, but this is just a bit annoying -- when I script
>> it, I end up with a bunch of "#temp.top.1#" etc files in my working
>> directory if I use editconf in the normal way, which is why I was
>> using the temporary directory thing to begin with.
>>
> Hi David,
>
> plz submit a bugzilla with all input and scripts.
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 12 May 2007 14:03:11 +0530 (IST)
> From: "Anil Kumar" <anil at chem.iitb.ac.in>
> Subject: [gmx-users] Error while running MD in DMSO!
> To: feenstra at few.vu.nl, gmx-users at gromacs.org
> Message-ID: <33690.10.103.7.2.1178958791.squirrel at www.chem.iitb.ac.in>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear All,
>
> I am running my simulations in explicit MeOH and DMSO. In case of MeOH, it
> is running fine but while running in DMSO.
>
> After running genbox i am having problem in running grompp for energy
> minimization.
> Error which i got is given below.
>
> Cleaning up temporary file gromppkkHvWC
> Fatal error: Atomtype 'SD' not found!
>
> Please, anyone let me know why it is happening when i had used the
> dmso.gro and dmso.itp files which is available by default to top folder.
>
> Thanks in advance.
>
> With Warm Regards
> Anil
>
> --
> (¨`•.•´¨) Always
> `•.¸(¨`•.•´¨) Keep
> (¨`•.•´¨)¸.•´ Smiling!
> `•.¸.•´
> «•´`•.(*•.¸(`•.¸ ¸.•´)¸.•*).•´`•»
> «•´¨*•.¸¸. * ANIL *.¸¸.•*¨`•»
> «•´`•.(¸.•´(¸.•* *•.¸)`•.¸).•´`•»
>
> ANIL KUMAR(Research Scholar),
> Bio-Organic Lab No-336(2nd Floor),
> Dept. of Chemistry,I.I.T.Bombay,Powai,
> Mumbai-400076,
> Ph. No.-022-25764780(Lab)
> -----------------------------------------
> Residence:-
> Hostel#1,Room#297,IIT Bombay,Powai,
> Mumbai-400076,Ph.No.:-022-25721017(Hostel)
> -------------------------------------------------
> Web:http://chemanil.googlepages.com/
> --------------------------
> "Education is a progressive discovery of our ignorance"
>
> - Will Durant
> ----------------------------
>
>
>
>
>
> ------------------------------
>
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