LISTSERV 16.0

Help for GLYCAM-L Archives

UGA Help Desk

Request a List


GLYCAM-L Archives

GLYCAM-L Archives


GLYCAM-L@LISTSERV.UGA.EDU


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

GLYCAM-L Home

GLYCAM-L Home

GLYCAM-L  March 2018

GLYCAM-L March 2018

Subject:

reading Idu2S generated by Glycam

From:

Tarsis Gesteira <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Sat, 31 Mar 2018 17:44:37 -0400

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (43 lines) , 1.pdb (43 lines) , 1.rst7 (43 lines) , 1.parm7 (43 lines)

Hi,

I'm having trouble reading a pdb generated by glycam. I created using heparin/HS builder

DGlcpNSa1-4DGlcpAb1-4DGlcpNSa1-4LIdopA[2S]a1-4 (GlcNS-GlcA-GlcNS-Idu2S-ROH)

When I try to read it back using leap:

 source leaprc.GLYCAM_06j-1   
 loadamberparams frcmod.glycam06_intraring_doublebond_protonatedacids
 loadamberprep GlcNS_preliminary.prep
 loadamberprep uronic_acids.prep
 loadoff GLYCAM_aminoct_06j_12SB.lib 
 loadamberprep IdoA_ALL.prep
 hepc = loadpdb 1_AMBER_noh.pdb

I get the following error:

Loading PDB file: ./1_AMBER_noh.pdb
ERROR: Comparing atoms
        .R<0YS 5>.A<C2 3>, 
        .R<0YS 5>.A<H1 2>, 
        .R<4ZB 4>.A<O4 19>, and 
        .R<0YS 5>.A<O5 16> 
       to atoms
        .R<0YS 5>.A<C2 3>, 
        .R<SO3 1>.A<S1 1>, 
        .R<0YS 5>.A<H1 2>, and 
        .R<4ZB 4>.A<O4 19> 
       This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL:    In file [chirality.c], line 142
!FATAL:    Message: Atom named S1 from SO3 did not match !

If I run the prmtop and crd though cpptraj it fixes the sulfate from the Idu at position 6 bringing it back to position 5. But I'm not sure that that's the way to do it.

Thanks for the help and happy Easter!

Best,

Tarsis

Top of Message | Previous Page | Permalink

Advanced Options


Options

Log In

Log In

Get Password

Get Password


Search Archives

Search Archives


Subscribe or Unsubscribe

Subscribe or Unsubscribe


Archives

April 2018
March 2018
February 2018
December 2017
November 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
December 2015
November 2015
October 2015
May 2015

ATOM RSS1 RSS2



LISTSERV.UGA.EDU

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager