[gmx-users] add a group to an amino acid
hengame fallah
hengame.fallah at gmail.com
Tue Nov 9 12:10:31 CET 2010
This is .rtp for [PHE] in opls:
[ PHE ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_149 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_145 -0.115 2
CD1 opls_145 -0.115 3
HD1 opls_146 0.115 3
CD2 opls_145 -0.115 4
HD2 opls_146 0.115 4
CE1 opls_145 -0.115 5
HE1 opls_146 0.115 5
CE2 opls_145 -0.115 6
HE2 opls_146 0.115 6
CZ opls_145 -0.115 7
HZ opls_146 0.115 7
C opls_235 0.500 8
O opls_236 -0.500 8
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CD2 HD2
CD2 CE2
CE1 HE1
CE1 CZ
CE2 HE2
CE2 CZ
CZ HZ
C O
-C N
and i got the charges by Gaussian.
I'm very confused now [?]
On Tue, Nov 9, 2010 at 2:13 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> On 9/11/2010 9:09 PM, hengame fallah wrote:
>
> Dear Mark,
>
> I edited my pdb like this:
> ...
> ATOM 41 N BOC 3 -1.862 5.210 5.333
> ATOM 42 H BOC 3 -2.325 4.344 5.618
> ATOM 43 CA BOC 3 -1.001 5.232 4.169
> ATOM 44 HA1 BOC 3 -0.540 6.235 4.026
> ATOM 45 HA2 BOC 3 -0.172 4.511 4.360
> ATOM 46 CB BOC 3 -1.797 4.794 2.924
> ATOM 47 HB1 BOC 3 -2.244 3.809 3.204
> ATOM 48 CG1 BOC 3 -2.976 5.730 2.589
> ATOM 49 CD1 BOC 3 -1.231 3.466 0.845
> ATOM 50 HD1 BOC 3 -2.070 2.790 1.081
> ATOM 51 CD2 BOC 3 0.120 5.408 1.353
> ATOM 52 HD2 BOC 3 0.357 6.277 1.986
> ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312
> ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964
> ATOM 55 CE2 BOC 3 0.881 5.182 0.197
> ATOM 56 HE2 BOC 3 1.706 5.870 -0.054
> ATOM 57 CZ BOC 3 0.591 4.093 -0.639
> ATOM 58 CG2 BOC 3 -0.935 4.544 1.698
> ATOM 59 HG1 BOC 3 -3.530 5.331 1.707
> ATOM 60 HG2 BOC 3 -3.708 5.729 3.431
> ATOM 61 C BOC 3 -2.565 7.148 2.291
> ATOM 62 O BOC 3 -2.716 8.035 3.131
> ATOM 63 Cl BOC 3 1.525 3.816 -2.062
> END
>
> and my .rtp file for [ BOC ] is:
>
> [ BOC ]
> [ atoms ]
> N opls_238 -0.500 1
> H opls_241 0.300 1
> CA opls_224B -0.005 1
> HA1 opls_140 0.060 1
> HA2 opls_140 0.060 1
> CB opls_149 0.140 2
> HB1 opls_140 0.060 2
> CG1 opls_145 -0.115 2
> CD1 opls_145 -0.115 3
> HD1 opls_146 0.115 3
> CD2 opls_145 -0.115 4
> HD2 opls_146 0.115 4
> CE1 opls_145 -0.115 5
> HE1 opls_146 0.115 5
> CE2 opls_145 -0.115 6
> HE2 opls_146 0.115 6
> CZ opls_145 0.885 7
> Cl opls_264 -1.000 7
> CG2 opls_071 -0.005 8
> HG1 opls_140 0.060 8
> HG2 opls_140 0.060 8
> C opls_235 0.700 9
> O opls_236 -0.700 9
> [ bonds ]
> N H
> N CA
> CA HA1
> CA HA2
> CA CB
> CB HB1
> CB CG1
> CB CG2
> CG1 CD1
> CG1 CD2
> CD1 HD1
> CD1 CE1
> CD2 HD2
> CD2 CE2
> CE1 HE1
> CE1 CZ
> CE2 HE2
> CE2 CZ
> CZ Cl
> CG2 HG1
> CG2 HG2
> CG2 C
> C O
> -C N
>
> and still i got that error!
>
> Fatal error:
> Atom HB11 not found in rtp database in residue BOC, it looks a bit like HB1
>
>
> a) This structure is phenylalanine with *two* backbone methylene spacers,
> not the one you said in a previous email
> b) Your charge groups are wrong (e.g. number 2)
> c) Your charges are doubtful (CG1 is negative???)
> d) Your atom types are worth checking (should the two backbone methylene
> carbons have those types?)
> e) The atom ordering of the coordinate file and .rtp file need to match
> f) The atom coordinates do not correspond to the atom labels they are given
> - presumably you got another bunch of "long bond" warnings that you didn't
> include in your last email.
>
> Mark
>
>
>
> On Tue, Nov 9, 2010 at 1:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
>> On 9/11/2010 8:19 PM, hengame fallah wrote:
>>
>> Thanks Justin,
>> actually the protein that i want to simulate consists of two amino acids:
>> PHE and BOC
>> BOC is an unusual amino acid as you know.
>> It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to
>> PHE
>>
>>
>> So that probably means you'll have to pay care to the [bonds] section in
>> the .rtp file. The only bonds GROMACS knows about are the ones in the .rtp.
>> They have to be right. The errors below look like you haven't done it right.
>>
>>
>>
>> I finally defined a residue BOC in opls .rtp file:
>>
>> [ BOC ]
>> [ atoms ]
>> N opls_238 -0.500 1
>> H opls_241 0.300 1
>> CA opls_224B -0.005 1
>> HA1 opls_140 0.060 1
>> HA2 opls_140 0.060 1
>> CB opls_149 0.140 2
>> HB1 opls_140 0.060 2
>> CG1 opls_145 -0.115 2
>> CD1 opls_145 -0.115 3
>> HD1 opls_146 0.115 3
>> CD2 opls_145 -0.115 4
>> HD2 opls_146 0.115 4
>> CE1 opls_145 -0.115 5
>> HE1 opls_146 0.115 5
>> CE2 opls_145 -0.115 6
>> HE2 opls_146 0.115 6
>> CZ opls_145 0.885 7
>> Cl opls_264 -1.000 7
>> CG2 opls_071 -0.005 8
>> HG1 opls_140 0.060 8
>> HG2 opls_140 0.060 8
>> C opls_235 0.700 9
>> O opls_236 -0.700 9
>>
>> the ending part of my PDB is:
>> ...
>> ATOM 38 HE2 PHE 2 -6.946 8.455 4.409
>> ATOM 39 CZ PHE 2 -5.456 10.015 4.624
>> ATOM 40 HZ PHE 2 -5.887 10.646 3.828
>> ATOM 41 N BOC 3 -1.862 5.210 5.333
>> ATOM 42 H BOC 3 -2.325 4.344 5.618
>> ATOM 43 CA BOC 3 -1.001 5.232 4.169
>> ATOM 44 HA1 BOC 3 -0.540 6.235 4.026
>>
>>
>> HA2 is missing here, per your .rtp
>>
>>
>> ATOM 45 CB BOC 3 -1.797 4.794 2.924
>> ATOM 46 HB1 BOC 3 -2.244 3.809 3.204
>> ATOM 47 CG1 BOC 3 -2.976 5.730 2.589
>> ATOM 48 CG2 BOC 3 -0.935 4.544 1.698
>> ATOM 49 CD1 BOC 3 -1.231 3.466 0.845
>> ATOM 50 HD1 BOC 3 -2.070 2.790 1.081
>> ATOM 51 CD2 BOC 3 0.120 5.408 1.353
>> ATOM 52 HD2 BOC 3 0.357 6.277 1.986
>> ATOM 53 CE1 BOC 3 -0.471 3.236 -0.312
>> ATOM 54 HE1 BOC 3 -0.717 2.381 -0.964
>> ATOM 55 CE2 BOC 3 0.881 5.182 0.197
>> ATOM 56 HE2 BOC 3 1.706 5.870 -0.054
>> ATOM 57 CZ BOC 3 0.591 4.093 -0.639
>> ATOM 58 C BOC 3 -2.565 7.148 2.291
>> ATOM 59 O BOC 3 -2.716 8.035 3.131
>> ATOM 60 CL BOC 3 1.525 3.816 -2.062
>> ATOM 61 HA2 BOC 3 -0.172 4.511 4.360
>> ATOM 62 HG1 BOC 3 -3.530 5.331 1.707
>> ATOM 63 HG2 BOC 3 -3.708 5.729 3.431
>>
>> Now i got t this error:
>> ...
>> There are 1 chains and 0 blocks of water and 3 residues with 63 atoms
>>
>> chain #res #atoms
>> 1 ' ' 3 63
>>
>> All occupancy fields zero. This is probably not an X-Ray structure
>> Opening library file /usr/share/gromacs/top/ffoplsaa.atp
>> Atomtype 1
>> Reading residue database... (ffoplsaa)
>> Opening library file /usr/share/gromacs/top/ffoplsaa.rtp
>> Residue 57
>> Sorting it all out...
>> Opening library file /usr/share/gromacs/top/ffoplsaa.hdb
>> Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb
>> Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb
>>
>> Back Off! I just backed up topol.top to ./#topol.top.69#
>> Processing chain 1 (63 atoms, 3 residues)
>> There are 3 donors and 3 acceptors
>> There are 4 hydrogen bonds
>> Checking for duplicate atoms....
>> Opening library file /usr/share/gromacs/top/specbond.dat
>> 7 out of 7 lines of specbond.dat converted succesfully
>> N-terminus: NH3+
>> C-terminus: COO-
>> Now there are 3 residues with 68 atoms
>> Making bonds...
>> Warning: Long Bond (52-53 = 0.334847 nm)
>> Warning: Long Bond (52-55 = 0.334912 nm)
>> Warning: Long Bond (63-64 = 0.271173 nm)
>> Warning: Long Bond (63-65 = 0.347808 nm)
>> Warning: Long Bond (63-66 = 0.31288 nm)
>>
>>
>> This is telling you the connectivity in your .rtp doesn't match the
>> spatial arrangement very well. Go back and check the .rtp file.
>>
>>
>> Opening library file /usr/share/gromacs/top/aminoacids.dat
>>
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 4.0.7
>> Source code file: ../../../../src/kernel/add_par.c, line: 233
>>
>> Fatal error:
>> Atom HB11 not found in rtp database in residue BOC, it looks a bit like
>> HB1
>>
>>
>> pdb2gmx is probably hopelessly confused by now. Fix the other issues and
>> try again.
>>
>> Mark
>>
>>
>> -------------------------------------------------------
>> ...
>>
>> What should i do?
>>
>>
>>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101109/6a9ca469/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 361.gif
Type: image/gif
Size: 226 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101109/6a9ca469/attachment.gif>
More information about the gromacs.org_gmx-users
mailing list